It depends on what you think the effect is on his character. If you think that without God, a person must be immoral, then break it off. If you think he can be a good person even with his beliefs, then you might keep going.
I don’t know if you are on marriage track, but if you are, then there should be a discussion about the kids and whether they will go to church or have a choice.
The thing that always kept me from having a relationship with people who believe in God is that I think they have a significant defect in their thinking. I.e., they had magical thinking and couldn’t see the world for what it is. I couldn’t be involved with someone like that, because I could never predict what they might do. I believed I would have a dreadful time associating with religious people, too.
If you think one has to be crazy to be an atheist (or whatever), then perhaps you shouldn’t be involved with him.
But I have discovered that religious people don’t necessarily behave as their religious texts suggest they should. The often lead quite sensible lives, belying their stated beliefs, and not even seeing the contradiction. They can be interesting and sensible when not discussing religion. Perhaps, from your point of view, atheists could be the same?