That makes them no less dark. Let's look at when they took place: Between the days of the Roman empire (a period in time when academia was sought after throughout the entire world, where science flourished and medicine saw daily advancement) to the middle-ages as you call them (a time of oppression and intolerance of other faiths where science and medicine were almost destroyed at the hands of the church) and into the Renaissance (the second age of enlightenment when science and medicine rose again).
Did you know that in the time of the Roman empire there were battle surgeons who had a detailed understanding of the human body and how it worked but that their knowledge was lost after the fall of the empire when their papers were burned due to their "heretic" content?
Out of the three time periods, the days of Rome were where one empire took control and said, "We're in charge but locally do as you please." The middle ages was the church going, "My way or die-way." and Renaissance was the age of, "I wonder what happens if I pull this... Oh, I'm doing this for God, really."
Ironically, the first one atheists were accepted, the middle one we were tortured and slaughtered, and the third one we had learned to hide ourselves and make snide remarks from behind the drapes.