You should find out more about what kind of church she goes to and what impact Christianity has on her daily life. If she goes to one of the more liberal "mainline" Protestant churches she may be more accepting of your atheism. If she goes to a more conservative church you may have a problem. Some conservative Protestants won't date non-Christians so you might strike out if that's the case.
I would say there's no harm in being honest.
I would say there's no harm in being honest.