Don't fret. A friend of mine was raised and married mormon then he came into the atheist light. His wife really struggled with it at first but they seem to be working it out now. They can even make little jokes about the others beliefs without hurt feelings. She still takes the kids to church but they also get to hear his side, so they will be able to make their own choices when they get older.
I guess what I am saying is that love can overcome many obstacles in a marriage... even a big fat book of lies.