One issue that was not raised in the recent Torah U'Madda discussion on Lookjed was whether academic study itself is a threat to religious belief. This was the topic of discussion in a recent interview that appeared in Biblical Archaeology Review, entitled "Losing Faith: How Scholarship Affects Scholars." In it, four Bible/archaeology scholars were asked whether their professional study in a field that held potential discrepancies with their beliefs affected their religious devotion.
Lawrence Schiffman was the (Orthodox) Jewish representative in this conversation, which is subtitled "2 who did and 2 who didn't." I will let you in on his conclusion (he did not find that his studies led him to lose faith), but the conversation is an interesting one.