You've been had my friend.
The first universities were not established by the church. They coalesced around guilds, teachers, students and were based upon the Hellenistic schools of Plato and Aristotle(the platonic acadamy was closed in the 6th century by the eastern orthodox church, derp). They were student supported institutions. It wasn't until long after their establishment that they were "founded" by the church in an effort to control them. Even among the monks it wasn't graduates of monastic schools that pushed science forward, it was the ones that also attended academies and universities established by the people that had use for them. It wasn't religion. It was guilds. It was real world utilitarian education and the demand for it that created universities.
Don't believe me? University of Bologna/Paris/Oxford, it's the same story.
Platonic tradition did not make its way back to Europe until WELL into the middle ages through the spread of Islamic scholarly work. Here's the wikipedia section of roots of universities in Medieval Europe:
The university is generally regarded as a formal institution that has its origin in the Medieval Christian setting.[4][5] Prior to the establishment of universities, European higher education took place for hundreds of years in Christian cathedral schools or monastic schools (Scholae monasticae), in which monks and nuns taught classes; evidence of these immediate forerunners of the later university at many places dates back to the 6th century AD.[6]
With the increasing growth and urbanization of European society during the 12th and 13th centuries, a demand grew for professional clergy. Before the 12th century, the intellectual life of Western Europe had been largely relegated to monasteries, which were mostly concerned with performing the liturgy and prayer; relatively few monasteries could boast true intellectuals. Following the Gregorian Reform's emphasis on canon law and the study of the sacraments, bishops formed cathedral schools to train the clergy in Canon law, but also in the more secular aspects of religious administration, including logic and disputation for use in preaching and theological discussion, and accounting to more effectively control finances. Learning became essential to advancing in the ecclesiastical hierarchy, and teachers also gained prestige. However, demand quickly outstripped the capacity of cathedral schools, each of which was essentially run by one teacher. In addition, tensions rose between the students of cathedral schools and burghers in smaller towns. As a result, cathedral schools migrated to large cities, like Bologna, Rome and Paris.
Some scholars such as Syed Farid Alatas have noted some parallels between Madrasahs and early European colleges and have thus inferred that the first universities in Europe were influenced by the Madrasahs in Islamic Spain and the Emirate of Sicily.[7] Other scholars such as George Makdisi, Toby Huff and Norman Daniel, however, have questioned this, citing the lack of evidence for an actual transmission from the Islamic world to Christian Europe and highlighting the differences in the structure, methodologies, procedures, curricula and legal status of the "Islamic college" (madrasa) versus the European university.[8][9][10]
And it is true that eventually universities started to emerge organically from need for professional training (in large part demand for professional clergy!). But the Church recognized them, financed them, protected their secular autonomy from political interests, forced them to include math and science in their syllabus, protected student and master free speech and gave them immunity from state prosecution, and later established publishing houses to spread scientific papers all across the continent (and did tons more actually). It really requires ignoring all the evidence in existence to deny the role of middle ages Christianity in pushing science forward.
History is complicated, and the world isn't black and white, and neither is the role of the Christian church. Anyone can cherry pick facts in order to confirm an established bias, but an objective look at history shows that The Church played a role in advancing knowledge that easily dwarfs its role in suppressing it.
I know you poopood the book recommendations written by secular historians of the Middle Ages, but I'll give a link to a nice article on the subject for those interested in a quick factual account of the time.
https://www.quora.com/Why-did-science-make-little-real-progress-in-Europe-in-the-Middle-Ages
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