However, I think Hannibal has genuine emotions for her. Like Abigail, though, he won't hesitate to put her down if she stands in his way whatsoever, or is in a position to expose him. I don't think he would prefer that option. Though, on that note, we don't really know if Abigail is actually dead.
I'll also add, that, as she's said in a recent episode, she's known Hannibal longer than ANYONE; Will, Jack Crawford. And she has managed to NOT sleep with him. Up until the last episode. And as every Dane knows, he is the sexiest man in Denmark, so, I know it wasn't easy. If she's projecting or transferring (she probably is, they're like besties, or at least she thinks so) it happened before getting it on with the Devil.