FairMormon is a non-profit organization dedicated to providing well-documented answers to criticisms of LDS doctrine, belief and practice.
Question: How has the Church responded to issues related to Church history?
Dallin Oaks: "Don’t depreciate their effectiveness in one area because they have some misbehavior in another area"
Elder Dallin Oaks discusses the issue of church history and facts that are not discussed frequently in church approved curriculum during an interview with Helen Whitney (HW) for the PBS documentary, The Mormons. He gives a good description of this dilemma and the church's method for confronting it. 
Referring to the importance of not focusing on a person's negative aspects while learning of their history Elder Oaks said,
...See a person in context; don’t depreciate their effectiveness in one area because they have some misbehavior in another area — especially from their youth. I think that’s the spirit of that. I think I’m not talking necessarily just about writing Mormon history; I’m talking about George Washington or any other case. If he had an affair with a girl when he was a teenager, I don’t need to read that when I’m trying to read a biography of the Founding Father of our nation.
Elder Oaks is then asked how the church deals with imperfections of early church members and current members coming across this information themselves on the internet rather than through teachings of the church. Elder Oaks responds,
It’s an old problem, the extent to which official histories, whatever they are, or semi-official histories, get into things that are shadowy or less well-known or whatever. That’s an old problem in Mormonism — a feeling of members that they shouldn’t have been surprised by the fact that this or that happened, they should’ve been alerted to it. I have felt that throughout my life.
Dallin Oaks: We’re emerging from a period of history writing within the Church [of] adoring history that doesn’t deal with anything that’s unfavorable
There are several different elements of that. One element is that we’re emerging from a period of history writing within the Church [of] adoring history that doesn’t deal with anything that’s unfavorable, and we’re coming into a period of “warts and all” kind of history. Perhaps our writing of history is lagging behind the times, but I believe that there is purpose in all these things — there may have been a time when Church members could not have been as well prepared for that kind of historical writing as they may be now.
On the other hand, there are constraints on trying to reveal everything. You don’t want to be getting into and creating doubts that didn’t exist in the first place. And what is plenty of history for one person is inadequate for another, and we have a large church, and that’s a big problem. And another problem is there are a lot of things that the Church has written about that the members haven’t read. And the Sunday School teacher that gives “Brother Jones” his understanding of Church history may be inadequately informed and may not reveal something which the Church has published. It’s in the history written for college or Institute students, sources written for quite mature students, but not every Sunday School teacher that introduces people to a history is familiar with that. And so there is no way to avoid this criticism. The best I can say is that we’re moving with the times, we’re getting more and more forthright, but we will never satisfy every complaint along that line and probably shouldn’t.
LDS Apologist Michael R. Ash makes similar points and adds helpful context in his book Shaken Faith Syndrome:
Betrayal and Church "Cover-Up"
When potentially troubling information is presented in faith-promoting ways, the information--accompanied by the weight of a faithful context--often helps members understand difficult issues within a framework of their belief system. When hostile sources present the same information, they frequently claim or imply that the Church hides this information from members. The critics supposedly are exposing a "cover-up". This may add weight to the contra-LDS source and give the impression that they (the critics) are really the objective truth-seekers who are merely uncovering the facts.
[. . .]
Information can be withheld intentionally or unintentionally. First we will discuss the intentional reasons. In the context of early creations of LDS history, we find a tradition among most-nineteenth century biographies (the primary form of historical creations) that emphasized the positive aspects of heroic figures in the hopes of inspiring readers while often exaggerating or even fabricating anecdotes--such as George Washington chopping down his father's cherry tree. Frequently, in cases of early American biographies involving religious or philosophical movements, the movement took center stage and the "history" was a tool for evangelizing the movement. Any information that might harm the movement was withheld from the biography/history.
Early Mormon historians, like many historians of their era, were not trained in history but were instead influenced by the English Puritans whose histories were written as faithful explanations of their events. These Puritans (as well as early LDS historians) believed that, like the Hebrews before them, they were God’s chosen people whose coming to America was part of God's unfolding plan. "Their history and biography" note three prominent historians, "told the saga of God's dealings as seen in their personal lives. In short, Puritan biography and autobiography were simultaneously scripture as well as history". "Accuracy and realism were...largely things of the future".
[. . .]
As for the unintentional censoring of information, we turn to the Church curriculum. Some ex-members complain that they never heard certain aspects of Church history from the Sunday School classes they attended. The purpose of Church curriculum, however, including Sunday School, Priesthood, and Relief Society, is to support the mission of the Church: to bring people to Christ. Very little actual history is discussed in Church classes. Even every fourth years when the Doctrine and Covenants is taught (which includes some Church history) the primary goal of the class is to help members draw closer to God, seek the Spirit, and understand gospel principles.
Ash then makes points about how many details about Church history that members "didn't" (or don't) "know about" are covered in Church magazines and other publications sponsored by the Church. He then discusses history reading in general in the United States.
It [has] been said that America is a nation of non-readers. We are, by and large, literate, but we are often [uninformed] and tend to spend less time reading than watching TV or surfing the Internet. A 2011 survey, for instance, found that the average U.S. adult spends about 7-12 times more time watching TV than reading books. Studies indicate that in the past two decades about 25% fewer American adults spent time reading books. According to another study,
- One-third of high school graduates never read another book for the rest of their lives.
- 58% of the U.S. adult population never reads another book after high school.
- 42% of college graduates never read another book.
- 80% of U.S. families did not buy or read a book last year
- 70% of U.S. adults have not been in a bookstore in the last five years.
- 57% of new books are not read to completion.
When we do read, we often choose pop magazines or novels over nonfiction. Most Americans, for example, are severely uninformed in regards to significant historical issues, current events, or scientific facts. According to a 2003 Gallup poll, a full 83% of Americans could not name the then-current Chief Justice of the Supreme Court, William Rehnquisy, and nearly a third of Americans were unable to name the then-current vice president Dick Cheney.
[. . .]
One recent study showed that many Americans were significantly ignorant on what should be common matters of religious knowledge. Only 54% of respondents, for instance knew that the Koran (Quran) is an Islamic holy book. Only 51% knew that Joseph Smith was a Mormon, and only 46% knew that Martin Luther inspired the Reformation. Althought the vast majority of the people polled [were] Christian, only 37% said they read the scriptures at least once a week...and only 45% knew that the Gospels [were] comprised of the books of Matthew, Mark, Luke, and John.
[. . .]
While General Authorities are typically well versed in the scriptures, they may or may not be very well versed in Church history. As historian D. Michael Quinn explains, "Church leaders have as much experience with the church's past history as anyone who graduated from seminary, so they are not trying to conceal any concerns or a great secret or mystery, because they are not aware of them. If they haven't acquired a knowledge of church history before they become General Authority, they don't have time to acquire it."
[. . .]
As we examine other challenging issues in LDS publications we find that many, if not all, of the issues have been noted, examined, or discussed by believing LDS historians in a variety of LDS-targeted publications, conferences, and programs. The Ensign and its forerunner, the Improvement Era (official LDS magazines) have the primary goal of enhancing member understanding of gospel principles and providing articles on how to implement those princples into everyday lives. Nevertheless, both magazines have run articles on challenging issues. Likewise, greater details on less commonly known LDS historical issues are found in the Church sponsored BYU Studies and other LDS-related publications. Following are examples of the issues tackled by these official publications. The Kinderhook Plates, Joseph's use of a "seer stone" to translate the Book of Mormon, Joseph's method of translating by putting the seer stone in the bottom of a hat and then putting his face into that hat, Joseph's early treasure digging, the Danites, the Mountatin Meadows Masacre, the Word of Wisdom in nineteenth century thought, a limited geography for the Book of Mormon, "other Amerindians” coexisting with Book of Mormon peoples, and more. LDS Scholars have openly discussed these topics for decades and any student seriously interested in LDS History had access to material that engaged these issues. Contributors to FARMS (the Foundation for Ancient Research and Mormon Studies, now the Maxwell Institute for Religious Scholarship) have been publishing books and articles on many in-depth and challenging aspects of LDS history, archaeology, scientific research, and apologetic issues since 1979. Ironically, many publications that are critical of traditional accounts of Mormon origins often withhold information that supports the traditional accounts. By presenting only unfavorable evidence and censoring the favorable evidence, much anti-Mormon material is guilty of the very thing with which they charge the Church--concealing the truth.
[. . .]
The confusion of Church History "cover-up" and "betrayal" may be best described as a complex issue involving many parties and different concerns and cannot be blamed on any one party nor one aspect in particular.
- The context of writing hagiographic histories and the world emerging from that period of history writing into the "warts and all" period. This includes the recycling of older materials into newer ones and creating a perhaps more widespread, yet less nuanced and less complex, understanding of Church history.
- The natural tendency of many to not be interested in engaging history--much less in a detailed and complex way. Most members aren’t interested in Church history or apologetic issues unless they need to be.
- Church leaders not being able to know many aspects of Church history with little time to research it other than occasional looks into the most preponderant books--recycling narratives that aren't entirely accurate.
- The concern with knowing when and how to publish information officially and where to focus discussion (whether in Sunday School, Relief Society, Seminary, or/and Institute) when it is made known and consensus has been reached among scholars as to its validity so that doubts aren't created where they weren't meant to be fomented. And
- The availability of information on nearly every critical issue in official magazines, semi-official publications (such as the Encyclopedia of Mormonism) and in publications by organizations sponsored by the Church (such as BYU Studies and FARMS) and organizations arisen without official sponsorship (such as FairMormon).
Thus, critics who would like to suggest that the Church has undergone a series of coverups to hide its "damaging origins" will have to go through pains to assert such. Conversely, it would be difficult for a defender of the Church to suggest that everyone should know about all of the issues in their complexity and be familiar with the resources discussing them (even though there are several examples of people who were and are), for such has not been the case with many popular materials discussing history at the most widespread levels (as demonstrated by point 1, Mike Ash's comments, and Elder Oaks' comments).
It seems as though, with regard to historical issues and critical questions, the Church is acting to centralize the information and moving it from an "if you need it" basis (as we have seen from the past) to full, upfront inoculation (as we are seeing now) which will hopefully eliminate future confusion. With the publication of the Gospel Topics Essays, the new narrative history being published on the Gospel Library, lds.org, and the Ensign called "Saints", the publication of the Joseph Smith papers, the introduction of courses such as Foundations of the Restoration in Institutes and Seminaries (which require the reading of the Gospel Topics Essays), and the digitalization of all of Church archives for public consumption and use, the goal of writing history "for the good of the church, and for the rising generations that shall grow up on the land of Zion, to possess it from generation to generation, forever and ever" will be accomplished well. We shouldn't worry about the publication of all of these resources. The Lord promises that "— there is no weapon that is formed against [us that] shall prosper" (D&C 71:9).
- Dallin Oaks, "Elder Oaks Interview Transcript from PBS Documentary," Newsroom (20 JULY 2007) off-site
- Michael R. Ash "Shaken Faith Syndrome Second Edition Expanded & Revised" FairMormon Press, 2014; pg. 12-17