I don't think the Apple is a PD case at all, and as has been mentioned, Kirk did try to leave, but was prevented, so because another highly advanced race has already interfered with these people and now directly threatens with the Enterprises ability to leave we should just up and die because of the PD says we can't interfere. No, I don't think the Apple shows Kirk violating the PD.
Errand of Mercy and Fridays Child, private little war, would seem to be cases where it is nice if we can avoid interfering with the local people, but if we don't' the Klingons will interfere them into slavery, so also cases where the PD would not be in effect.
I don't really think there where many cases where Kirk and company came upon a civilization advancing normally without interference from other highly advanced cultures. They probably did from time to time, but they where just too boring to make an episode out of.