But then who could have killed her? Madara already seems stronger than the Juubi was so that doesn't really leave any possible adversary for her.
Well you know me wild theories and all, like I've said before I think her sons sealed her in the moon and she is still alive. Probably with her thoughts seeping into the minds of the decedents of the elder son, The curse of the Sharingan. Without knowing it her thoughts have been implanted into their minds as if they were their own. It's how Madara came up with the Moon's eye plan and why Obito said he wanted to become complete. Maybe this is done with subtle genjutsu/ Psychic driving.