it doesn't need to be an issue. don't get all up in her face about it; if she gets all up in yours, and you're not cool with that, break it off. you can respect her choice to believe without having to believe yourself; if she's worth your time, she'll respect that.
(oh, btw, athiests that go around preaching their superiority are just as arrogant and annoying as the nuts that go around trying to "save" people by conversion to <religion of the month>. fyi.)