I remember the first time I learned some of the challenging aspects of church history. The massacre at Mountain Meadows, details of polygamy, multiple accounts of the first vision, and etc. I felt doubt stirring in my mind and heart. It was painful, but short lived.
On reflection, I now realize I assumed the Lord’s appearing to Joseph Smith meant the Lord was there 24/7 guiding the restoration. Consequently there could be no imperfections in the establishment of the church, or in the lives of those who carried the work forward, therefore church history would be uncomplicated and without blemish.
I wonder why I entertained such naive notions. I was a student of the scriptures and understood the difficulties the Savior had with His hand picked apostles. The Book of Mormon’s first family (Lehi and his wife Sariah, and their children) certainly couldn’t have contributed to my naïve ideal. The Standard Works of the church attest to the frailties of mankind, and nowhere teaches the ideal that church history, ancient or modern, ought to be uncomplicated and blemish free.
I read an article by a LDS church historian who didn’t mince words about the silliness of getting caught up in the problems of church history. Davis Bitton, a prominent LDS historian makes the salient point that those who know our history the best, church historians, remain faithful committed members of the church. He wrote:
Let’s get one thing clear. There is nothing in church history that leads inevitably to the conclusion that the church is false. There is nothing that requires the conclusion that Joseph Smith was a fraud. How can I say this with such confidence? For the simple reason that the historians who know most about our church history have been and are faithful, committed members of the church. Or, to restate the situation more precisely, there are faithful Latter-day Saint historians who know as much about this subject as any anti-Mormon or as anyone who writes on the subject from an outside perspective. With few exceptions, they know much, much more. They have not been blown away. They have not gnashed their teeth and abandoned their faith. To repeat, they have found nothing that forces the extreme conclusion our enemies like to promote… Competent historians who have devoted many years of study to the issues have not felt compelled to abandon their faith in the restored gospel…
Think not when you gather to Zion,
Your troubles and trials are through,
That nothing but comfort and pleasure
Are waiting in Zion for you.
No, no, ’tis designed as a furnace,
All substance, all textures to try,
To burn all the “wood, hay, and stubble,”
The gold from the dross purify.
When Eliza R. Snow penned those words, they were good advice for the emigrants leaving Europe to join the Saints in the West. Similar counsel is sometimes needed by students of our LDS history. “Think not when ye study church history,” we might sing, “that everyone was always smiling, that the women were always dressed in freshly laundered, starched pinafores, that the men spoke softly, grammatically, and always politely, or that the children were well mannered angels.” Think not! In other words, get real! 
In my opinion, those who get hung up on issues in church history and claim this is reason for doubting, not believing, having their name removed from the records of the church, or not joining the church have other options available to them. For me it was found in prayer and study. Go here for my story
Following is additional information for those interested in this subject:
* YouTube-Davis Bitton Here
* F.A.I.R.-Davis Bitton Here
* Meridan Magazine-Davis Bitton Here
 It was shorted lived for me because I had been the recipient of many manifestations of the Spirit. All that I needed to do is reflect on these experiences and the doubt and pain I experienced were swallowed up.