This isn't something that's personally affected me at work yet, but it is happening to someone I know right now.

His boss his very Christian, while my friend is an Atheist. This boss keeps starting these one-on-one discussions during lunch that go along the lines of, "It's amazing how complicated x is - there's no way we could possibly be able to do that or explain it ourselves", to which my friend will side-step the statement with something like "lol not yet!" and try to change the subject. The first time they had a discussion like this (which again the boss initiated), my friend got more "into it" than he realized he probably should have, and it left a bad taste in both his and his boss's mouths. Ever since then he's tried to avoid any kind of discussion about religion (or the lack thereof), but his boss won't let it drop. Today my friend even went so far as to say he didn't want to talk about religion at work, and his boss responded that to him, it wasn't a religious discussion, just "logic".

If I were in his situation I'd be freaking out, not just out of being furious but because of being scared to lose my job. I told him to document everything said, and told him any different treatment he receives, even if he's not fired, is still religious discrimination. It's not even right that he's being forced to have these religious conversations with his boss (who I should mention actually OWNS the company), but what can he do? Suing/lawyers cost money, and it's not like it's even gotten that far yet. It's just a nasty, precarious situation to be in, and it'd be nice to shut it down as quickly, quietly and amiably as possible. He doesn't want to leave the company anytime soon, and with this being his first career-oriented job out of college and only being there for a year, it's not like he could find another job that easily even if he decided to look. 

Any input would be valued and appreciated. Thanks!