this thing is all over the place.
but anyway, as others have said it's hard to distinguish between religion and politics for much of history. Religion certainly is an excellent catalyst for oppression and violence right now.
I don't hear that many atheists talking up about the inevitable collapse of religion, I hear hope for it, and anything that indicates it does get promoted, but most atheists are more worried about it getting stronger if anything.
but besides this how is making this a popularity contest going to help anything? (though that net loss seems suspicious, from what I understand global growth is fairly flat)
Europe's dark age was a time of ignorance and superstition, mainly due to the collapse of education as a result of de-urbanization. all of the worlds knowledge was in books few could read. religion was a highly effective tool for controlling the ignorant masses, keeping the serfs in line. this was the time and place that defined all of the typical anti-religious cliches and ties back into that whole "hard to separate religion from politics back in the day" thing.
one thing I would like to specifically address though is I find calling anyone from this time or earlier a scientist highly questionable, these were 'natural philosophers'. you cannot name any oppressed scientists prior to 1500 because there really weren't any of them, science is a fairly new thing. now what I would like to see is a listing of people from 800-1500 in Europe who proclaimed anything significantly opposed to Christianity on any sort of (preferably natural) philosophical grounds. Religion retards science not (typically) by opposing it wholesale, but by making it culturally/politically impossible to teach truths that are not inline with said religion.
That last one, though perhaps technically right on some presented details, is fairly wrong in the bigger point, there were TONs of similar mythological figures historically. not that I consider it important, but I said something about all the other points.