Exactly. I would imagine that the knowledge that the Federation regards the necessity of killing everyone on a planet so likely that they have a General Order regarding it wouldn't go over too well.
Kirk did object for a second or two but fell in line fairly quickly. And when his ship was targeted, legitimately as the Federation had no business being there when they were warned away, then he took it upon himself to totally disrupt the civilization on not one but two planets. Imagine that the promised negotiations fail and it leads to all out nuclear war. What would the Federation say then? Whoops?
If either Eminiar VII or Vendikar had asked for Federation assistance then it's a different story. However, they were there simply to establish a treaty port, regardless of the wishes of the systems inhabitants.