I think the main point here is that an atheist can pretend to be religious, and nobody can tell. Or to be more specific, if it is to the religious group's benefit, sometimes they don't care if the person believes or not.
Suppose you were to survey those congregations where the minister realized they did not believe anymore, and asked them if they wanted the pastor to a) tell them the truth and let the chips fall, to b)keep pretending for the good of the church, or to c)sneak away under cover of darkness and leave the church in disarray. My guess is that most of the people--fine, upstanding Christians-- would prefer that the atheist minister b)live a lie and keep on doing their job.
I have read some of the responses from religious people about the truth project and that is what a lot of them say. "Why couldn't the pastor just keep on working at the church?" and "Why did they have to make trouble?" and "If nobody could tell, why should the pastor care?"
Honesty and integrity be damned. Just don't make me uncomfortable.
Of course those are the more polite reactions. Others are of the "Who cares about the fact that you no longer have a job? It's your own damn fault!" and "You were never really a Christian!" and "I hope you burn in hell forever!" variety. The prospect of a loving Christian reaction is why there are probably many more atheists hidden away in priest, nun and minister robes.
If it is a Muslim cleric, however, they know they face death if they dare to suggest that they no longer believe.....no truth project for them. They would have to have plastic surgery, change their identity and go into witness protection from their loving flock.
Added later http://www.npr.org/2012/05/07/152197685/when-religious-leaders-lose-their-faith
Among many supportive responses from non-believers you get NPR being criticized by Christians for even running the stories esp. Without giving "equal" time for the many atheists who have become religious
and see comments like this from religious folks: "When someone turns their back on God or disregards him it can be nothing other than rebellion against God or the idea of God. Plain and simple." Plainer and simpler: there is no god.