Universities were created, and existed, to train men to read Latin and to argue using Latin rhetoric. They did this by having the students read the best available pieces of ancient literature and rhetoric. You needed these skills in order to read the Latin Bible, and to argue theological point using the rules of Latin rhetoric. When ancient Greek was reintroduced to the system, Greek became the third pillar of a classical education. This means that a well trained clergyman knew the Bible, Latin literature, and Greek literature, and a system of rhetoric to argue in this arena.
However, the Bible and ancient literature had limitations. How do you argue about new things? The answer to this practical problem was the Scientific Method, which allowed people interested in new topics a way to argue those topics where no Biblical sources are applicable, and where no ancient Roman or Greek sources are applicable. Since you can not use rhetoric to demonstrate your point, as there is no pre-exising authority, you must have some system in which to argue. Where you have no authority, you must have a way to build authority, and a way for others counter-argue your authority with their own authority. Thus, we get the scientific method. You propose an explaination (a theory), you demonstrate support for your theory, and others can verify what you argue, modify it, or build competing theories.
The less well recognized purpose of the scientific method is its avoidance of theological matters. If you have theories, you want to argue those ideas without running afoul of church censors. So, the scientific method only uses natural agruments, which gives a researcher a fair degree of safety when publishing in a church dominated system. By avoiding theological arguments, you avoid heresy. You avoid censorship, as the censors have no cause to censor you. Book publishers will print your work, as they are safe. This worked fairly well. This worked so spectacularly well that the Age of Reason emerged, and the rhetorical methods in science were adopted by the religiously based universities. In other words, religion embraced the scientific method, rather than reject it.
There are a few areas where the scientific method did run afoul of religion. The first was cosmology. The solar-centric model of the universe ran afoul with theology. The second part was natural history. These two created the worst social and theological firestorms. Cosmology got sorted out first. That fancy new solar-centric math allowed the Church's relatives to navigate the world and get rich. In time, the clockwork arrangement of planets became an argument FOR God, rather than against, and everyone settled back down. The same is not true for Evolution.
Interestingly, quantum phyics has created no religious controversy. This is very odd, as quantum physics pretty much relegates Darwin to a warm-up act. However, "Einsteinian" doesn't have the ring of "Darwinsist".