Considering that he's asking for help on the basis that he had already come out to his father as an atheist shortly before joining the site, I think it's a bit late for this sort of advice. From his introductory post:

After I told him about this, he handed me a book (The Reason for God by Timothy Keller) and signed himself up as a counselor for something called The Clash, described as a Christian "worldview conference". Next week, from July 30 to August 3, he's going to take me to this big huge realignment thing, and I'm worried I won't be able to defend myself.

So not telling his family about his atheism is really not on the table.

He could pretend to recant, which would help preserve his father's opinion of him in the short term, but it's possible that this deception will make Benedict even more uncomfortable with their relationship than overt disagreement. There is also a danger that this will hurt his relationship with his father even more in the event that he comes clean about his atheism at a later date.