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...that may not solve anything but will get the budding atheist through the next couple years:
1. Keep quiet and graduate.
2. Do not tell the parents. Lie to them. For the rest of their lives. They don't need to know.
3. Be sensitive when telling the friends. If they truly care and respect him, they will accept him as he is. If not, he may as well make more open-minded friends anyway--either in addition to or in place of the current ones.