Hmmm...I don't often read mysteries—personally fantasies are more intriguing, but I've read a few mysteries. The first that comes to mind would be The Mysterious Benedict Society. It was utterly fantastic—the only thing I think is important for you to know is that Trenton Lee Stewart (The author) is, as far as I know, not a Christian. I liked his books anyway, though there is, I think, maybe two references to a witch. I keep my eyes open for these kinds of things, so it's not that the whole series is about witchcraft. I think he once says someone's hair is flying around wildly, and they looked like a witch. (though that may have been in one of his other books.) It does not have witches in the storyline, unless you include the fact that one of the main characters sometimes has scary dreams because of a medical condition he has. I will say that I had read the first few books of a series by Chris Colfer. The long and short of it is that God told me that wasn't something I should be reading! Hehe. But, yeah. Just wanted to let you know. You know what would be the best sort of thing for you to read. That said, I really enjoyed Trenton Lee Stewart's books, and they were, as you may have already guessed from the title, mysterious.
Whew......that was a lot..