My bet is that if your kid is asking questions (note - I don't have kids so I might be wrong) he should have those answered from both of you and being given the choice to believe on or another. Personally my girlfriend is a Christian and I'm an atheist, I will not have a problem with our future kids going to church as long as the indoctrination is not overly severe, I guess I'll just look for a different priests, I've met one or two I wouldn't mind letting my kids being with since they pose questions from a critical thinking/philosophical perspective and not only with Christianity.
Whoever fights monsters should see to it that in the process he does not become a monster. And if you gaze long enough into an abyss, the abyss will gaze back into you
