She will be fine.
I'm an atheist and I've always said that my biggest hypocrisy is that I send my daughters to Catholic school. I live in South Louisiana and I couldn't in good conscience send my kids to any of the public schools around here. The one in my district had a valedictorian that couldn't pass the exit exam a few years back, they are that bad. With that said, I have one daughter in high school and one still in elementary school and despite having religion class and going through the Catholic motions, they aren't religious at all at home. It isn't reinforced at home at all and we teach them to be skeptical but respectful. For the record, I'm not "grooming" my children to be atheists, I just want them to have the ability to make up their own minds without being overly brainwashed before they have that ability. They ace their religion classes but so far both have been asking the "right" questions at home showing that they are indeed remaining skeptical.
Remember, this is from a life of Catholic school and not a single year of pre-K where they can barely even broach the subject in a way the kids can understand.
Edit: The irony among ironies is that Louisiana passed a law that is claimed to allow the teaching of Creationism. Yet both of my daughters Catholic schools, that don't need permission from the state, teach evolution in science class. That was a deal breaker for me and I asked science teachers in both schools and both apologized and said something like "yes, it's a very well-documented theory and we would be hurting the kids teaching them that it's wrong. They were assuming that I was going to be upset about them not teaching creationism in science class and were very relieved when I assured them it was the opposite and they didn't have to have "that" argument again.