And, maybe he did misinterpret the pope. But I still think rest of the "imaginary drama" was probably meant to be humorous. In fact, there's quite a bit of humor in the book. There's the story about the wager he had with another collegue (the one where subscriptions to Playboy and Private Eye were the stakes), and, if you have the illustrated edition of "A Brief History of Time," he has an astronaut falling into a blackhole to demonstrate how they work. So I think too much was made of his statement.
You are probably right that altho Hawking is a great physicist, we should not take too seriously his philosophical and historical statements. Also I am sure you noticed he concludes Brief History by predicting one day we might "know the mind of God." Of course what he is talking about is not "God" but about scientific knowledge becoming so all encompassing that it could explain the movement of material particles in all circumstances - which for him is all there is.
It is interesting that while he praises Galileo for freeing science from religion, (a debatable claim, see: footnotes to Bottom Line) Hawking seems to want to subject religion to science. He is not alone - our whole culture tends to do that by equating naturalist philosophy and science.
Fr. Phil Bloom
P.S. Do you have access to New Oxford Review? The June issue has a good article on the "Galileo Legend." You may have heard the story about clergy refusing to look thru his telescope. Turns out it was actually his scientific rivals (Cremonini & Libri) who wouldn't do it, but that two priests, Frs. Clavius & Grienberger did and were converted to Galileo's Copernican position. So there are dumb scientists and smart priests in every century!