Religion vs. Science in the 14th Century

In 1348, the black death ravaged western Europe. At the time, there was very little scientific knowledge about disease, epidemiology and bacteria. There was very little the medical community could do. Instead, the people of Europe looked to the religious. In that, a fanaticism was born. The worse the plague got, the worse the ideology became in its vain attempts to defeat it. The most extreme of this was a group of Flagellationists who took to the streets, marching from village to village, showing their devotion to God by whipping themselves repeatedly in penance of their sins (and perhaps spreading the plague even further with their travels).

Their actions seem incomprehensible to us, because we possess a greater understanding of our surroundings, albeit incomplete. When a civilization does not understand, it seems to seek solace in religion. If the sun did not rise tomorrow, and our scientists could not understand it, would we be any different?