Same type of situation with blowing up the Universe in the 'Big Bang' , who benefits from that? I'm guessing we will never find out.
I still say it was Omega. He has a documented grudge against the material universe. He would destroy it just for spite. Heck, he already tried to do that once in "The Three Doctors."
Alternatively, it would have to be someone else outside of the universe who wants the universe destroyed. My timey-wimey theory is that it's the original 11th Doctor. Think about it: The original 11th Doctor went through the crack to seal it up at the end of "The Big Bang." The Doctor that we've seen since then is a copy created from Amy's memories. What if the original Doctor were still out there in the space outside of the universe? Suppose he'd grown angry and bitter over the eons seeing this new "impostor" running around living his