There's also how Sekai was recently restored before this, and shown up on the roof in the same reset that Yumi seemed to die in:
So, it seems to be alluding that she is responsible for it. Why Yumi and not Maya, then? Not sure. It could mean that there are worse plans in store for Maya, and they might involve Ayane replacing her.
As for Makoto, I think it could go either way. Unlike Yumi and Tsuneyo, Sensei has defiled Makoto, so that seems to increase her chances of surviving quite a bit. In retrospect, that might be the reason Yumi was taken out. Being a virgin might be a death sentence in this horror film.