Funny you should say that Brainbob.
The Communist Party of Kampuchea (ie the Khmer Rouge leadership) were among some of the most educated minds of southeast Asia, with many of them having doctorates from the University of Paris and the University of Phnom Penh. And then there were the
various Nazi leaders who had genius level IQ, and although Brainbob doesn't consider that a true measure of intelligence, many of them also graduated top tier universities with honors.
Of course this is where he pulls some bullshit about how these men's intelligence was all fake and "purchased" despite their formidable achievements in politics, organization, and at least in the Nazi's case, inventions, because he can't admit to the simple facts that intelligence doesn't equal morality and that highly intelligent people can still make horrible mistakes.
His moral paradigm is that those who are highly intelligent (i.e., think like Bob) are good and pure, and those who are stupid (i.e., don't think like Bob) are evil. He's gone on and on about how "intelligence is the only virtue," and that gets him into hot water sometimes when people call him out for being ableist. He'll usually try to backtrack by claiming "I didn't mean
that kind of intelligence" without actually clarifying what he means. I do think his belief basically boils down to "if you agree with Bob, you're smart," coupled with some general "fuck yeah science" bullshit.
But just taking him at his word that he actually does mean that smart people are automatically good, my rebuttal is that intelligence is more of a modifier on how much good or evil one can do. Generally speaking, someone who isn't very intelligent won't get very far in life, and thus the amount of people they can impact is fairly low. While they won't be able to help many people, they also won't be able to hurt many either. But someone who is intelligent will be able to use their smarts to get ahead, rise up to positions of power, and have influence on hundreds, thousands, or even millions of people. The amount of good or evil an intelligent person can do will generally be much higher for that reason.
The biggest problem that I have with Bob's mentality is that many of these intelligent people think that they know what's best for those around them, inflicting their desires on others "for their own good." As you've said, many an atrocity has been committed by those of high intellect, all because they thought they were doing the right thing. I could repost that C.S. Lewis quote again, but you get the point. Being smart in one area does not make you automatically smart in all areas, and it certainly doesn't convey moral authority.