Board Thread:Naruto Discussions/@comment-25139119-20141009153023/@comment-17623-20141009154835

Chibaku Tensei does not kill her. She can't actually die, she is functionally immortal. It can however keep her trapped inside it for titans knows how long, especially since it is now in a dimension that nobody else can get to.

Black Zetsu needed to impale and merge with Madara because, for whatever reason, Kaguya was not able to transform back into herself after going full Ten-Tails. I don't know why. I don't much care. But for whatever reason, Black Zetsu needed the chakra taken from the victims of the Infinite Tsukuyomi and someone pretty much close to her body to regain "physical form".