Wow, that's rough, Dragonfly. You kind of have to go out of your way (and pay private school fees) to send your kids to a religious school in the US. So unfortunately, I don't really know what it's like there. I think I would contact the school with my questions and concerns. But if you think that might just make your children more of a target, then don't.
Sheesh, for all the wailing and moaning the religious do about their beliefs being under attack, it always seems like they're the ones making it hard for everyone else.