On A, maybe. On B: zetsu clones revert to a zetsu body after being killed and C, well I already explained the genjutsu thing.My theory..
A) Either rin was captured and controlled by Madara, forcing kakashi to kill her in order to activate obitos mangekyo as part of his master plan.
B) It was a Zetsu that appeared to look like Rin, which would still activate Obitos Mengekyo via Kakashi
C) Either Rin or kakashi was under a genjutsu and still kakashi killed rin in order to activate obitos mangekyo as part of madaras master plan.
Either or, I still think Madara had something to do with it.