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.