I appreciate your situation, and understand your point about it being a "big deal and not an issue at all." Because it shouldn't be--yet, on account of the majority opinion, it tends to be treated like a huge issue, despite it not having to be one to you.
I know having a child complicates things; my wife, after her recently being "saved" decided to start taking her almost 4 year-old daughter (my stepdaughter) to church. I love this little girl, and have openly spoken with my wife as to why taking her to be taught guilt and shame at the altar of this supposed loving religion would be a bad thing (though much more kindly put). But this seems to have no effect. This, among other things, has caused my relationship with my wife to drift apart, though I seem to be doing almost nothing to cause this rift to widen (she continually tells me how sad she is that I am going to hell, etc., and religion seems to be the wedge she keeps hammering deeper between us). I am slowly coming to accept that things are probably heading to a point of terminus with her, and that really freaking sucks. I'm not sure really how to cope with it, but I am not going to just lie to her and pretend that I believe in something I would be lying about.
I can't discuss my take on the world with damn near anyone, because if I tried in this State they would treat me like I'm crazy. That's why I came to this site, in the hope that I might meet at least a few people who have some kind of curiosity about the world around them and are not afraid to question their fundamental assumptions about the world.
I don't know exactly where I'm going with this, except to say that I feel for you, I'm sorry you are having to face this situation, and that you are not alone. I hope your significant other matures, but a lot of the time religious people don't, as I've regrettably found out.
I think you have a lot of courage to face this situation, and I hope things turn out well, one way or the other. It sounds like you are doing the best you can.