You're in a rough spot, especially with a small child. Not for nothing, but I really think you should see a marriage counselor. You may have to travel a bit to find one who won't automatically take the religious person's side; it's your relationship that needs the help, not who you are. If it doesn't work, if she can't accept you for who you are, at least you'll know you gave it your best shot. And if she can't accept you, that doesn't necessarily mean that she's in the wrong, it is a very hard adjustment to learn to love the person a spouse becomes when it's very different from the person they fell in love with and chose to marry. Some couples pull it off, my partner is something like a lapsed Bahá'í but still a theist.
I'm not anti-Christian. I'm anti-stupid.