I would like to hit a few points, and will try not to get carried away:
1) Much of the belief that "the Medieval Period was a Dark Age stagnated by religion" stems from arguments of the Protestant Reformation and after, where Protestants argued that science and progress was held back by a church rooted in mystical rituals. For example, the well known idea that before Columbus the world was thought to be flat. Progress before the reformation was ignored, so as to avoid giving credit. This was beneficial for obvious reasons, as the argument showed protestantism as based on logic and reason and catholicism as a backwards mystic religion to be avoided. This view became widely excepted, certainly in the english-speaking world.
2) I would actually argue that religion encouraged scientific advancement, stemming from the middle ages. Philosophers and Scientists felt compelled to study nature because it was a way of studying and understanding God's creation. For example, Roger Bacon, Thomas Aquinas, and Descartes.
3) With the chaos that occurred with the final sacking of Rome, the collapse of the Western Roman Empire, and the mass influx of war-like tribes, nearly all institutions collapsed. Christianity, in the form of the Church, was really the sole institution to remain. It can be persuasively argued that it was the backbone from which Western Europe climbed back from the ashes. Others have touches on this.
4) With the security of the Roman Empire gone, regions and towns internalized their trade and small feudal states emerged. This "Dark Age" was fueled by neighboring fiefs and kingdoms raiding each other's land, razing crops and property, stealing livestock, etc. Not sure how society is expected to progress under such conditions.
5) What rate, exactly, was society supposed to develop at without religion, or in the historic case of Europe, Christianity?
On a related note, and this is speaking much more generally:
6) I think people have a tendency to be arrogant about the past, believing that we are so much better, so much more moral, ethical, civilized, whatever, than those who came long enough before us as to not be in personal memory. Today we look at the middle ages and say, "1200 AD? What a bunch of backwards goobers. They had no concept of reason and believed in magic hocus pocus". People aren't stupid and never have been. I don't think we give our ancestors much credit to their intelligence.
