Well, with the Duras thing, the Klingons aren't Federation members so that might change things. Plus, I thought he attacked Duras?
As for the rest of the conversation, I have a feeling there is probably stuff in The Federation Charter that recognizes traditions of the member worlds, even if they do contradict other parts of the Charter.
I thought the whole thing with Ardana was that the Federation did not know about the Troglytes?