Either side has a case within context of their own principles so how is it decided which one is right?
Contact the Excalbians.
But seriously, I'd really like to know the details of the Organian Peace Treaty. Considering the Organians didn't want outsiders to interfere with their business (and probably gave the Federation a lecture of their Prime Directive) I'd think it would stand to reason that the peace treaty also included a prime directive for planets disputed by either two. How the Organians ensured that both sides would honor the treaty, is a different can of worms.
Regarding Kirk's actions prior and during ST II I couldn't help but to mention this
in the Excelsior
scaling thread (and Timo disagreed).
Considering that the Talos IV incident had been filed (what good is the threat of the death penalty if no one knows it exists?) I'd assume that the same applied for Ceti Alpha V.
Vonda McIntyre's novelization of TWOK suggested that Reliant's
crew was so burned out (and close to mutiny) trying to find a suitable Genesis test planet, that somebody simply overlooked this decisive detail.
So who was responsible for the entire Mutara Mess? Blame it on the deceased Captain Terrell, Chekov, the Reliant's
science officer (Kyle?) or Kirk?
Did Terrell sacrifice himself not only to save the life of Kirk but in full awareness that he would be blamed and no other member of his crew?