Spock was quite surprised that anyone could admire Khan in "Space Seed" and described him as a "Ruthless Dictator". Whether or not Scotty was accurate to say there were "no massacres" or that McCoy was right about there being "no wars of aggression" is up to interpretation. People say things like that about everyone from Alexander to Bonaparte, but they're only half-true. What Alexander did to Thebes for example, or Bonaparte's treatment of the slave rebellions in the Caribbean are by our standards today genocidal. That they're not described as such often speaks more of their historical romanticism inherit in European narratives of their leaders than the reality. I'm pretty sure there's an element of that lurking in what the human members of the Enterprise
crew were saying.
The evidence we see from Augments and the horrors of the Eugenics Wars as described in every episode, like Spock noting that whole populations were bombed out of existence, and that Khan himself was going to be tried for war crimes.
And being "the least brutal" of a group of aggressive genetically engineered dictators isn't much of a qualifier. I'm inclined to trust Spock's word on his description as a dictator and a ruthless one at that, over that of the fawning humans.