True enough! I'm a christian with mild synesthesia. I don't think I ever thought about how it might relate to my beliefs before, but I guess it's no different from anything else that can differentiate each of us. Whatever we do, whoever we are, we should try the best to make use of our abilities (or quirks, as some might think of it) for God. How that specifically applies to synesthesia, I don't know.
I don't think of synesthesia as super-natural, and I don't think there are any references to it the Bible. I'm actually not sure it's really that big of deal, one way or the other. More of just an interesting quirk that some of us have. I guess I'm glad I have it? I don't really know what it's like not to have it though. I've always suspected it's a lot more commonplace than most people think.