The Prime Directive had to at least come up in conversation when first contact with the "Private Little War" natives was discussed. They definitely were a pre warp civilization.
Well to be fair their mission end seemed to be just to study some of the planets for medical reasearch or something and they probably weren't even planing on talking to the locals until they showed up ans shot Spock with guns they weren't supposed to have yet.
After that Kirk took the liberty of trying to blend in on the next trip down while he was investigating just what the hack was going on.
Also the Prime Directive did factor into it, Kirk only told the one guy he was from space a swore him to secrecy about it, his wife only found out from watching McCoy use a phaser.
Plus it seems some form of a Prime Directive like rule was part of the Organian Peace Treaty as the Klingon Empire's advancing one of the faction was a violation of the treaty.