Graham Harman has a post on Hawking's new project. I think it's admirable for philosophy to question scientists, often and early. Off the top of my head, I see two problems with Hawking's basis for atheism:
1) Gravity has to exist in his view—the Universe is thus not strictly arising from “nothing” as he specifies. Some kind of object(s) already existed.
2) Gravity may well be epiphenomenal to the Universe. New research at Berkeley is wondering whether quantum level phenomena are a kind of picture of the very early Universe, just as deep rocks are pictures of the early ages of the Earth. Gravity, famously, doesn't square with the other three fundamental forces one finds there. If you treat gravity as emergent, you get rid of a lot of other problems such as the massive imbalance of dark matter to matter.
3) (addendum) This means that space–time is not a continuum all the way down. Strike one to Aristotle...