I'll admit that's the problem I have the most trouble with, but after the debacle in the Library she may have felt like he didn't care, and / or be steeling herself to prove that she can be as calculating and strong as Harry.
On the other hand, it may all just be wishful thinking on my part. But it does explain:
1) the beginning of the scene in the Library (with Hermione desperately searching for a way out of the debt) 2) Harry's casual mention of the fact that he's not sure whether it will absolve him of the debt or not 3) Weasley brain wipes 4) Dumbledore's persistent absences
Plus it would firmly establish Hermione as Harry's equal, putting the boot in on various speculations about HPMOR being sexist in what I can only imagine would be an extremely satisfying fashion, from Eliezer 's pov.
I have to write it somewhere - because what is the point of a belief that does not allow you to make predictions that you are willing to stand by - and I guess this is the place. I believe that Hermione is not dead (duh!), and planned this all for the purposes of getting Harry out of his debt to Malfoy and/or preventing herself from being used as a weapon against Harry. She used or was discovered by Fred and George who were subsequently memory charmed by Dumbledore, who has spent entirely too much time off-camera of late.
Edit: I'll add that - on the odd chance I'm right, and this ends up sounding like bragging - I don't think that makes me particularly clever; I think it speaks to skillful but subtle hinting on the part of the author.
Particularly since, given Harry's investigations into the pouch, "Hermione's body" or at the very least "Hermione's transfigured body" should fetch it for you no matter what you've hidden it as. The pouch isn't an extra way of hiding something, its a particularly handy way of finding hidden things.