@jasonwolf - I agree that they very likely have a complicated relationship. I'm on board with the idea that Leon has a very good idea that
something unusual is going on with Morgan - maybe he's seen her get injured and shrug it off in a way that just doesn't seem right, or something similar. It would be
difficult to come across concrete information suggesting she's anything but what she presents as (Much of her life with the FBI is classified, though that isn't an insurmountable obstacle), but the totems might have a kind of amalgamated indication, if he were to put the pieces together.
In terms of a hunter and hunted, though, Morgan isn't really the kind to turn on Leon if he did decide to start pulling on threads. That would likely be more a case of "Well, Mr. Smith. Let's have a drink, you and I. It seems we both have cards to put on the table."