I think you've had some brilliant responses on here, haven't read of them yet though!
I appreciate your approach and that you think you are teaching her choice to abstain from something from which she disagrees but i actually think it could be more beneficial to her to stick the classes out.
There's rising intolerance for people expressing different views and beliefs and we all need to get better at dealing with this. If she stays in classes, she'll be learning tolerance first hand and it will stretch her critical thinking- both of which are absolutely invaluable skills. Especially if she wants to go to university in the future, where much critical thinking requires people to carry a line of argument through to the conclusion, even if it doesn't represent their personal views.
I'm always surprised when I meet other atheists who express so little tolerance for people of religious beliefs. Your point that religious ppl don't have a monopoly on being good is correct, but equally they don't have a monopoly on being 'bad', wrong or intolerant.
I have many friends who clearly have religious beliefs when I get to know them and yet are obviously wary about expressing these in public which I think is really sad. We're all allowed to say what we believe without being accused of forcing it on another person. They're also lovely, tolerant people. Being Christian, for example, doesn't necessarily mean you believe gay ppl are going hell.
So often, the tendancy I see among fellow atheists is that the attitude of refusing to have part in discussion in which their beliefs are shared just shuts them down flat. Sure, if anyone expresses any opinion which is extreme you walk away but we all need to learn to respect each other and put views and part of that is in learning about them.
I think you'll be missing a trick if you pull her out of classes and she can gain so much more from being part of them simply because she doesn't believe.
I'd encourage her instead to increase her learning, so if she feels classes are limited and one sided continue the research you do and show her the others sides of the story. I think you're doing a great job - keep it up!