It has also been hundreds of years of Western history since the intellectual class was driving this "punishment", and that was when religion and education were tightly linked.

The problem isn't that ideologues are new, it is that ideology has seeped into the highest levels of education and culture. You have people across the spectrum of disciplines and stances afraid to contradict the received knowledge of the masses (or one of usually two sects).

This hasn't been the case for a LONG TIME.