Wasn't there a story about someone who accidentally Polyjuiced herself into a cat and, instead of getting help, hid from the teachers, so she got stuck cat-like? McGonagall could turn into a cat and Polyjuice herself into Hermione from that state, to get the effect deliberately. The waxy, doll-like appearance could be a side-effect of deliberately botched Polyjuice. Or... Hermione could Transfigure McGonagall. Hard, but quite possibly just within her capabilities, with guidance.

The ward message is a problem, but, as jaibot suggested, maybe McGonagall enrolled herself as a student. Or maybe the wards sound the same for students and teachers, and Dumbledore interpreted it when he saw "Hermione" dead.

The description of the death scene is Harry's interpretation, not objective truth.

At this point in the narrative, I can add epicycles to deal with the problems, which is just as it should be. It is a beautiful theory (and my baby!), and I still have a few hours before the really ugly facts show up.

Edit: And here they are. The tragedy of theories strikes again…