Yeah, if the kids are being tested on the content of the material and the teacher is giving them different answers, that's a problem. I would instruct my child to pay attention to the MATERIAL!!! Study what the book says and block out what the teacher says about the age of the Earth and fossils, etc. In the meantime, I would press on the counselor. If you keep at them, they'll have to do something. Explain that it's not necessarily her beliefs that are the problem, it's the contradiction between what the books say (which is what they'll be tested on and does the school really want to have an entire class do poorly on them???) and what the teacher is telling them.
I agree that each person is entitled to their religious beliefs, for sure. I wouldn't even care if the teacher told her students what her beliefs are, if she felt it necessary. However, she is a science teacher. She is supposed to teach science, whether she agrees or not. A history teacher would have to teach about the Holocaust and wouldn't, hopefully, agree with it. It's important our kids are given opportunity to explore these areas and be given truthful information. Keep talking to the counselor and principal, they can't ignore you forever.
Good luck!