I earned a degree from BYU some time back. I knew many LDS people who did not truly believe in the tenants of their religion, but they were as unquestionably LDS as those with strong conviction. People simply believe what their parents believe. In political science, it is a widely known fact that ideological socialization(IS) is acquired overwhelmingly through the immediate family. The percentage is high enough to spawn entire sub-fields trying to find out how else is ideology acquired(as obviously many people break away from their parents beliefs). Being part of a community affects almost all aspects of one's life. Like someone mentioned above, he sticks with the system simply because he believes it strengthens his family and imparts good morals on his children. In reality, of course, he's judging those virtues through his own IS. I for an example, do not think that Christian moral ideals are as desirable as secular ones. Thus, I would not value the part religion would play on their imparting.
Breaking away not only forces a whole new paradigm on a member of a species that values stasis over flux, but also requires giving up many important things. Most communities, even tolerant ones, have prejudices against dissenters, and changing views is in practice ostracism from one's niche.
What I'm trying to say is that specifics on why someone leaves are, in a way, irrelevant. Every person has doubts on the truthfulness of one's own ideology. Rejection of an ideology happens when whatever brain mechanism is responsible for evaluating information decides the downsides of leaving a religion are preferable to sticking with it. The actual intellectual justification for leaving typically evolve significantly, after the departure.
While I think I understand what you are saying, to me that is all that is relevant. While you may be right about the big picture, when I am dealing with people I choose to zoom in and focus on one person at a time. With each person, the specifics are all that matters. If looking at the big picture as I think you are, specifics may not be that important. I use "may" because I'm not informed enough to know one way or another, but I trust you. I do wonder though that whatever brain mechanism is responsible for evaluating information might care about the specifics in order to make whatever decision is made. Just thinking out loud.