With respect to making your decision, I would advise you to just spend more time with her. It usually took me about 18 months to figure out how I would finally feel about someone, long-term, that I was initially attracted to. After that period of time, differences were either sources of annoyance (or something more neutral) or sources of contempt. If the latter, for either one of you, you're "too different". (Things are complicated by the fact that there's always a little contempt in a relationship, but the contempt I'm talking about will tend to grow and feel more important than everything else over time.)

In other words, I don't believe, a priori, that in order to be consistently rational, a rationalist should seek out another rationalist. You're probably seeking someone that complements you, and pushes you to more fully experience life, and that's why opposites attract. As long as you have the same core values about what matters to you both. It takes time to determine if you share those.

Regarding the magical thinking that perplexes you: it doesn't seem to me that most rationalists actually understand what it is that magical thinkers believe. For example, if you think about it in terms of scientifically true and false, you're probably not thinking about it the right away. Magical thinkers know they're not making scientific statements. For example, it's not false to believe you have a soul. Whatever she really means by having a soul, she does have. That's why rational arguments don't work. I think it's a matter of communication: she's not really expressing what she means by soul, and you're not really arguing (if you were to) that what she doesn't have is the soul she's talking about. Her description of a soul may be naive and if she's says anything about it that is scientifically falsifiable, then she is confused about what she means. But whenever she gives a description that is not scientifically falsifiable, and you see it as false, you are probably interpreting the words in too literal a way. Magical thinkers make the same mistake as well, and there is a downward spiral of overly literal thinking when the original belief was just that there is some concept of self that is related in some complex way with the physical body, that has value to her and her community (religion).

I don't think establishing a rule "you won't try to convert her" is going to work well, as I personally wouldn't want to always (or ever) have to repress what I think. That's not respectful of either of you. Instead, another suggestion: use your rationalist skills to approach it as a research project, but expand your sources. Trying reading books written by really good theologians (for example, very logical ones) on whatever they have to say about the soul -- you may be able to find a description of "soul" for example, that you both agree on. And then the difference may just end up being that she has a context for valuing that concept, while you don't.