he started to talk about god made everything etc., which really freaked me out
Rather than being freaked out, it sounds like a perfect opportunity to talk to him about what you believe, explain to him that people believe different things, and tell him that he will gradually decide what he believes as he gets older.
If it was religious school, those lesson might happen regularly
So, more opportunities to talk about it at home and help your child to put what they're being told in context. So long as you (and the school) encourage open discussion, and make it clear that it's ok to ask questions, then there is nothing to fear. Problems arise when children are told to keep their opinions to themselves, usually by parents who were told the same by their own parents when they were at school. MEanwhile in the classroom things have moved on - schools have to respect the differing views, and everyone benefits from hearing them expressed.
That is another reason why I think open admissions to faith schools are important. Yes, the majority may still be "of the faith", but everyone benefits from the presence of people with different views.