McCoy didn’t like it, but he also didn’t threaten to report Kirk to StarFleet as he would have if Kirk had suggested something in complete violation of regulations or morality.
The episode does not indicate that the policy implementation in this specific case was ultimately succesful, but I assume that we are supposed to think that Kirk knows what he is doing.
The Organians wouldn’t have cared. Even if you don’t buy that they only intervened in the Federation/Klingon war because the conflict had reached their territory and thus they were being disturbed, Kirk was taking the least violent option available to him. I suspect that the most Organia would have done would have been to toss Federation & Empire off the planet.
We never find out if the policy implementation was ultimately successful, at least not in the series; I’d not be surprised if one or more of the novels came back to address the issue. But I’ve always thought that Kirk was basically right; there simply was no good resolution available by the time Enterprise became aware of the situation. All he could do was take the least horrible.
I’ve always thought this the best of the original series episode. I especially like Kirk’s weariness at the end, when he tells Spock to beam them not up, but home. He wants to get the fuck off that planet, and even more than in the Edith Keeler episode, he knows that he’s basically failed to do good.
The episode was on the Space Channel just the other day:
KIRK: So, they’ve broken the treaty. SCOTT: Not necessarily, Captain. They have as much right to scientific missions here as we have. KIRK: Research is not the Klingon way. SCOTT: True, but since this is a hands-off planet, how are you going to prove they’re doing otherwise?
And a few minutes later:
KIRK: Bones, I’m as worried about Spock as you are, but if the Klingons are breaking the treaty it could be interstellar war.
Later, McCoy and Kirk go into the village to look for evidence of Klingon interference, as though such items are going to be presented to some sort of arbitration court. The only possible arbiters in this case would have been the Organians; no other power could come to a decision and enforce it.
Presumably, the treaty referred to is the Organian Peace Treaty referenced in “The Trouble with Tribbles,” but interstellar war isn’t a method of conflict resolution the Organians would have allowed. So Kirk is worrying needlessly in this respect.
If the Klingons (and now the Federation) were banned from the planet, knowledge of aggression would have remained among the inhabitants. The Organians (if they were so inclined) would then have had to take an active part in suppressing any further such actions. The alternative would have been to leave the Villagers and Hill People to their own devices.