It's hard to be yourselves in the relationship. Your values just don't match up, and that extends to your deepest beliefs on a spiritual level. You try to talk about the things that are important to you, but you've found that your ideals are not in the same ballpark at all.
If the relationship is important to you, you, especially, might be covering up your beliefs -- denying your ideals in an effort to save the relationship. However, there's no reason why clashing values or spiritual beliefs have to mean the end of an otherwise perfectly good romantic connection. Sometimes, the tension and stress created by an aspect like this one is enough to kill the relationship, but you two seem to have chosen to learn from it, and from each other, instead. This has taken a conscious commitment on both your parts, of course, which means identifying the problem as a couple and agreeing to work on it. This was, and is, harder than you expect. But you can come through it with a wider perspective of the world and of the spiritual possibilities open to you. However, as already stated, this is hard work; not something for the light of heart.