I'd be more worried about having kids. Your wife may, with time, accept that your religious beliefs differ from hers, but she's almost certainly going to want the children to follow her way, as you'll probably want them to follow yours.
I'm an atheist myself but I'm not yet convinced that's a good way to raise children. it may very well be that my wife and I (both atheists) choose to attend a church with our children. (Atheist parents are welcome to offer suggestions but there's no rush, children are a long way off for us.)
I realize that you love your wife (as I love mine) but it's possible this is an insurmountable obstacle. It really depends on how she feels about unbelievers, and what her church teaches about them. But children will definately be an issue here, if you plan to have them.
[This message has been edited by crashfrog, 01-26-2004]