Elder Wirthlin said in his wonderful talk, "Concern for the One", that some people leave the Church because they feel different - that they don't fit in and can't be accepted. As I have worked with those who are struggling with some kind of crisis of faith, his words have resonated deeply with me. The following is something that hit me recently as I was discussing this very topic with a group of friends:
Feeling like an alien is hardest for those who didn't feel like an alien for most of their lives. For someone who has spent years feeling comfortable and accepted and "normal" within the Church, it's extremely hard to go through a crisis of faith and suddenly feel like they don't belong anymore - and that is magnified and exacerbated when those around them downplay or criticize them for their change in perspective. What could have been a wonderful opportunity to grow a more mature and personal faith turns into a "conflict" that drives them away - and much of the responsibility for which way they go rests with those around them and how they react.
I have an advantage in a real way, since I've felt like an alien pretty much my entire life - and my "alien-ness" is related directly to how I view and interpret history, doctrine, scripture, etc. One of the reasons I can view myself as orthodox even though I have a number of heterodox beliefs is that I've been dealing with that paradox (being a peculiar person in an already peculiar group) for so long that it now simply is part of how I view my own condition of "I am".