As a fellow atheist, I sympathize with your situation. My wife is religious (not in a big way) and we got married in church. I was totally up-front with the religious people that I didn't believe a word of it and they actually didn't have a problem with that so I guess it just depends on their degree of fervour. No doubt this is why my wife's church is in such terminal decline!
Kids are obviously the big one and, I agree, there's going to be a lot of shuffling around in the pews if your's don't appear like clockwork every Sunday.
Honestly, I think this is one of those situations that is out of your hands. If it matters too much to her, there's not much you can do about that, and you just need to keep up communications on this issue so that any problem comes to light as soon as possible.
