This is a tricky one.

While I agree with the teacher's philosophy as a whole, it does seem as if he were injecting personal opinion into the classroom quite a lot, something that bothers me, because it could (and does all the time, in the bible belt) go the other way just as easily.

If a devout Christian had been censured by a court for constantly insulting evolution in a high school, we'd likely be cheering, but the reality is that neither should be taking place, at least not until college where, in a seminar format, students can hash it out.

He should be teaching facts, as science understands them, and leaving the question of religion out of it altogether, positive or negative. If the issue comes up, the appropriate response is that religion is a matter of personal belief, and is not a part of the curriculum. That's true separation. Then if Christians tried to silence him, they'd have had nothing to stand on.

Taking snarky shots at religion (while I find them amusing) wasn't helpful, and while I don't like the court ruling this way, he probably brought it on himself, giving them ammunition.