While I agree with your point, you're factually incorrect.
First, you're only talking about most of Europe and some of Asia -- not the whole world.
Second, no -- NOT all people believed in god. Yes, the church ruled, and so people who did not believe in god usually had to *pretend* to in order to avoid being burned to death, but there were still plenty of non-believers.
The big problem with the dark ages was that government and religion were so intertwined, and the churches had political power. That's a lesson we should all learn from and NOT repeat.
Peace.