Just a thought, but when Kakashi said eveyrone close to him as died, it could be meant as both figurativly and literally. Some/Most of his close friends could have just flat-out died, but some of them could also figurativly die, and in this case, Rin could be included. Like, after experiencing the events, Rin could have completely changed and her personality did a 180 turn, and in that way, the real Rin died... I don't konw, I could be grasping for straws here, but to me, she seems too much of an interesting character to be killed flatout and without any explanations...