I do not remember where Kirk violated the PD. Bend it like Picard, yes, not care about it, no. It is not like he let guys like Tracey who really violated the rule number one get away with it.
About flexibility, somehow the 23rd century Federation seems more harsh with the death penalty being implemented and so on.
The Apple - Even Spock told him.
Actually, all that was said that it
might be considered a violation, but it was never said to be actually.
Return to the Archons - destroyed the ruler of a society & fostered a revolution.
Friday's Child - Violated custom
Private Little War - Kirk becomes JFK/LBJ on Vietnam, following idea that domino theory = balance of power theory.
The Cloud Minders - Accused of and Guilty as well (kidnapping).
In all of these cases, Kirk was acting within the provisions of the Prime Directive as it existed at the time. But by the time of Picard, Sisko, and Janeway, the Prime Directive became much more conservative and many of Kirk's actions would have been considered violations by 24th-Century standards.