Falcon,
You're having the look of someone who knows what they think and is desperately thrashing around for confirmation. Your understanding of the middle ages seems entirely unidimensional, and honestly it looks like you're not even reading what you're posting.
Look at this:
The Spanish Inquisition was particularly brutal in its methods, which included the burning at the stake of many heretics. However, it was initiated and substantially controlled by King Ferdinand of Spain rather than the Church; King Ferdinand used political leverage to obtain the Church's tacit approval.
In modern culture, politicians cloak themselves in the flag to strngthen their position and power. In medieval times, it was the church.
What's more, you must remember that power hungry people migrate to power centers, and that meant the catholic church back then. Which means that a substantial number of priests and even popes called tehmselves christians but paid no attention to the teachings they supposedly believed.
Phillip of Spain was like Osama Bin Laden in his fervor and politics. (Not my compraison -- read it first in article in ?Military History?) To make it worse, he ran the greatest and richest power on earth, equivalent to USA now -- but without the EU and China to balance. The Inquisition (and his religious wars in the netherlands) were the expected result.
BTW, you mentioned Thomas Kuhn's
Structure of Scientific Revolutions -- and correctly remembered that he coined the phrase paradigm shift. The book may be particularly applicable to the thread overall -- one of his observations was that when new theories are proposed, which could replace common scientific wisdom, they generally are not accepted by those with vested interest in the old ways. Once the old scientists die off, teh young guns hold the field with the new ideas....
