Hermione, who is dead and whose body is gone

I tend to disagree. In fact, if you really meant to write "decayed", I think you're transparently wrong, because Quirrellmort wouldn't let it decay - he'd stick the body in box A (so to speak).

That seems like the main alternative to the obvious fulfillment of the ancient prophecy. I do worry about it, since why wouldn't Q have done this? (If he's figured out reflective decision theory, I'm officially confused about the direction of this story.) But if Harry transfigured the body quickly enough, he might have left Q without a good opportunity.