In one of my earlier relationships, my girlfriend wanted to be spiritual or Christian while I identified as atheist. It was an issue in the sense that I worried she was going to get "weird." I didn't really have anything against religion then except that it seemed people did weird stuff for no reason other than dogma.
Since we talked about having an open relationship, I was very worried about if she accepted Christianity or got more into it, that she would suddenly decide that polyamory was immoral. Or decide premarital sex was bad. (Her sister became a born again Christian and started speaking in tongues, seeing demons and believed in faith healing.)
I don't think she felt comfortable becoming more Christian around me because I would poke holes in the dogma. She felt that she would be in a constant state of defense of her religion. So we kind of agreed not to talk about it. But it turned into a wedge issue. In the end, she said that God told her that she should be with another man in a monogamous relationship.