If he is gifted and interested in science, introducing him to lesswrong, rationality and the Singularity could have a substantial positive impact on his academic development. What would be the worst that could happen?
If I understand correctly, your primary concern is that he may rationalise himself into this "belief in belief" situation, and that this will ultimately delay or deter completely his transition into atheism?
"I suspect this is why most people don't come out as atheists until after they've established separate identities from their parents and families.
A lot of people never escape from these traps." - What evidence do you have for thinking this? I would think that challenging religious assumptions at a younger age would result in an ear...
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