There is The Apple. Which I admit is a flat-out blasting away of the Prime Directive.
Not really. After all, the Triangulan natives didn't build Vaal. Presumably some outside civilization built it and imposed its rule over them. In Kirk's view, he was serving the Prime Directive by eliminating alien interference and restoring the Triangulans' right of self-determination.
"Kirk's view", a humancentric application of values and morals to an alien race is EXACTLY why the PD exists.
Further more, I would have loved to have seen a Star Trek ep where our heroes encounter a completly peaceful, loving nice race....more than willing to help our heroes....who keep slaves. And rather than get mad when our guys start stammering away, they just smile and nod and say, "Well, despite our differences, we're more than willing to extend our hand to you" (We kind of see this in that ENT PD ep, but they focused on that DNA dead-end nonsense)
Then we get to watch the crew argue and say how they should refuse aid ala VOY's "Counterpoint".