I don't fundamentally disagree on the overall strategy of the Catholic Church throughout the millennia, but it's also true that its position in the Middle Ages cannot be reduced as a "permanent inquisition". In fact, as you know the Inquisition itself didn't even exist before the XII century. I think the point that we all need to keep in mind is that the Church was fundamentally a temporal power back then, and behaved accordingly to ensure its own survival.

After the end of the Western Roman Empire, the Catholic Church was fundamentally an administrative body tasked with ensuring the continuity and overall coherency of the European way of life. As such, it was culturally conservative and focused on self-preservation, but could also be quite progressive whenever it suited its aims. Theological arguments were fundamentally political arguments, so the acceptance of this or that interpretation was strictly linked to the political needs of this or that time.

In this context, "heretics" were fought mercilessly whenever they became politically dangerous (or worse), but otherwise left alone or even engaged - many of the order-founding saints were "heretics" in all but name, barely paying lip service in terms of obedience to the pope. In modern terms, it was not unlike the ruthless treatment of Black Panthers in the context of a society otherwise focused on accepting increased equality for black people. If a big and strong Germanic tribe showed up with some quirky beliefs, they would be promptly "retconned" into Catholic doctrine if it ensured those tribes would pay their taxes to the Church. If a particular Pope needed to shore up support in this or that matter, he would accept novel interpretations. And so on and so forth - after all, any institution that can survive a thousand years is unlikely to always be consistent on almost anything.

It is true that it was also a brutal organization - they were brutal times, after all. The conquest of Italy by the Longobards enshrined in law the acceptance of revenge killings and bloody family feuds; the ruling classes were defined by their professional mastery of immediate violence; and Europe was the theatre of continuous warfare. Most Church personnel were drafted from the upper classes, bringing with them bellicose beliefs and a muscular approach to the exercise of power. It is somewhat unrealistic to expect modern attitudes to inclusivity from such times. Even the Ottoman Empire, at the time a beacon of tolerance, equality, and social mobility, ended up banning the dangerous printing press.

And yet, even in such difficult times, the Church ensured a level of cultural life survived. They established what were, in context, academic research bodies in a number of areas. Theological debate was not dead and fixed, but actually extremely alive and strong - most modern intellectuals would not survive a month in a medieval context, where the mastery of logic and recall was everything. Yes, you had to play by certain rules, but the skill necessary to do so while arguing against practices observed for centuries was massive.

It's a bit like contemporary China, where scientific and social progress is accepted and encouraged, academic prowess is prized, but you can't make any argument against the primacy of the Party or you get "disappeared". You can still bring about change (the various PCC heads have modified the orthodoxy many times), but you have to do it without threatening to burn down the house.

History is all about complexity, and reducing the role of the Catholic Church to Hollywood stereotypes is ungenerous.