(Spoiler) So, did Morgan know that...

...that Lee was like her? It seemed so to me. Their dialogues were pretty strange and when Lee is locked up in the room Morgan says to her: I'm starting to feel like myself, do you feel like yourself, Lee? or do you feel like something else?

And at the end, Morgan doesn't kill Lee,perhaps because she wants her to suffer?! (she was injured like the deer earlier)