I don't think Kirk and company would really worry about planet-bound, pre-spaceflight civilizations they found stumbling onto Khan and his gang. Certainly they'd not be concerned about the god-like aliens they encountered falling victim to him. As for space-faring civilizations at technological levels similar to the Feds, they really didn't encounter very many of them. Even so, I have a hard time believing Khan and his colony would represent any greater danger to, say, the First Federation than the dangers they would just naturally face by exploring space in the first place. I never make assumptions about the Original Series' intentions based on what the spinoffs cobbled together after the fact.