Kirk had been to the place before and was unaware of any troubles on the planet!

JB
Kirk was not aware of it--that's the key that's unavoidable. He is in the service of Starfleet, not the inner workings of the Federation until he--and his staff--reach that "need to know" level. That is how the real world military works in relation to administrations/state departments, etc. There is no shared knowledge about situations that do no involve the military until they need to know, if at all, hence the reason he had to learn about the Troglyte situation--by simply falling into the middle of a conflict. That said, it would be astoundingly naïve for anyone to believe a galaxy-spanning organization enters into relationships with planets for resources, etc., and
never learns a single thing about its business, production, beliefs, cultural practices. Its patently unrealistic, as it does not happen in reality, either (and for Western countries, flies in the face of basic national security protocols). Governments
pick and choose their opposition/outrage to partner countries' practices (which is why the
selective protestations of United Nations members is considered a joke by many nations), and are quite comfortable not revealing the abuses of said partner countries until it becomes a problem
for their interests.
Also of note, Plasus was full of confidence when he threatened to report Kirk for his interference--it its obvious he had a relationship with the Federation the 1701 crew was unaware of, and in making his threat, was sure they would side with him. The reason he would believe that is the Federation knew how Ardana was managed, and were content to let things stand. The only players out of the loop were the 1701 crew.
In the Ardana situation, Troglyte grievances were not a problem for the Federation, since the ruling government--despite Troglyte attempts at terrorism--were largely controlled.