Actually some of the greatest centers of learning throughout Europe were run by the church. The great libraries of antiquity were saved by the heathen muslims and much of the great sciences of the 8th to the 14th century were centered around universities in the muslim world also guided by the church. Who do you think taught DeVinci latin, math, and geometry in his early years, the church? Who paid his wages while he invented, researched, and created. His financial supporter while he lived was the church and king. Many of the greatest minds of history were taught and supported by the clergy.
Yes, the church did stifle aspect of learning, especially for the poor, but it also support many in their work, studies, and creations. Quiter often the building of a church was a major job creator for all. Few did it for free.
Your list of horrors are also looked at with the eyes of the 21st century and not contemporary eyes. Similar horrors were inflicted by non religious societies as well. We've had this, 'who killed more people, heathens or religious institution', before on TERB and you must have been asleep, as it wasn't even close.