So, how do we sail around the "now I know why they were conquered" thing?
SPOCK: My father's race was spared the dubious benefits of alcohol.
McCOY: Now I know why they were conquered.
In the writer's mind, so early in the series, it might have meant: "Spock is from a foreign planet, but he's speaking our language and serving in our fleet, so that means we conquered his people, took over, and civilized them."
But that was never going to fly, between Roddenberry's ideas of enlightened conduct and Nimoy's insistence that Spock be a powerful leading character. Therefore in universe, McCoy was surely referring to the whole Surak/Logic revolution as having "conquered" Vulcan. And Spock was wrapped up in a different subject, so he ignored the characterization. I think that's pretty smooth, as retcons go.