I can agree with this.
But you have to admit, for a teacher to specifically ban that phrase it sure looks like the teacher's intent is to specifically single out religion. There is really no good reason to ban it otherwise especially considering how you put it here, that it is an all-but-meaningless phrase that is really used as a social lubricant more than anything else. So why would the teacher single it out if not to take a jab at religion?
Taking a jab at religion... I don't know. "Religion" seems pretty quick to scream and holler when its overwhelming presence, dominance even, is mitigated in any way. This teacher has also banned "hang out" which also seems pretty damn petty. The phrase has meaning as far as common usage is concerned, even though the literal interpretation doesn't match. Maybe, just maybe, this teacher is trying to prove a point about the way we use language. It's also possible that she doesn't like public expressions of religious belief. It's even possible that both things are true at the same time.