I don't think I'd start by saying he's being unprofessional if I talked to him about it. I'd probably start by saying the amount of Christian theology being taught in class makes me uncomfortable (giving as an example treating the gospels as historical fact, or the like) and that I was wondering why it was being included. This tells the professor that you are uncomfortable with it but gives him a chance to explain why he's including it. He might actually have a decent reason -- it seems doubtful from the description given, but it's certainly possible.
Touche.