Exactly. Even in Paul Graham's own essay, some things are always forgotten. He's smart enough to question why the Church/Italian state attacked Galileo for repeating Copernicus' ideas, who was a celebrated hero of the church.
And nobody ever realizes that Galileo was not at all interested in the scientific facts (well he was, up to the point he went insane and became a political agitator and generally a lunatic, read his letters, you'll see that I'm actually quite polite here). Rather he was organizing demonstrations and violence because the church owed him a different kind of state (needless to say, with him on top) because the earth rotated around the sun (amongst many other "reasons", most of them quite insane). This case was then dug up later to justify ripping the catholic church out of Germany. That failed, but the story about Galileo stuck.
Some of our historical heroes ... aren't heroes. Socrates is a similar situation. Celebrated philosopher. Speaker at nearly every forum (meaning the weekly meeting where their direct democracy happened). He was an advocate, a statesman, a philosopher.
And then they execute him. Wait. What ? Nobody ever seems to think that they've probably skipped over small part of the story here.
An inaccurate summary was that Socrates' students were involved TWICE with actions that led to the military sacking of Athens, with very strong suspicions of him having ordered them to do so. This "just happened" to occur right after one of the first times he didn't get his way in the forum. The first time he got off with a stern warning, execution of every one of his students involved that sided with the occupying force, and a promise not to have any students for 2 years, which he promptly ignored. Then it very nearly happened again, and again his students were helping the enemy army. Then he was executed together with his students.
There is at least a decent case to be made that Galileo was executed for organizing violent protests against the state (using, amongst many other things, the idea that the earth rotated around the sun as a rallying idea).
Likewise, Socrates was likely killed for organizing the military conquest of Athens when he couldn't democratically get his way in parliament twice (and for having a habit of sleeping with the wives of other Atheneans). Not because Atheneans were afraid of science.
Neither of them were very nice people. Not that horrible people can't be important forces of good in history, but you should at least note that this is so. E.g. Kemal Ataturk, an early 20th century figure that a lot more genocidal than Hitler. He also ended the 1.5 millenia long war of muslims against the west and the east, and frankly without him we would not have a modern time. He ended it because he thought it was a waste of money, effort and most of all, lives, not because he was against war. He just didn't believe the objective was worth the cost. Still, his importance in making our current mostly democratic world possible is at least on par with Churchill. But he is a monster, personally responsible for several ethnic extermination campaigns, no doubt about that.