Actually, the dilemma which worries me the most-- since I get worn out trying to make sense of the Prime Directive-- centers around the Federation's willingness to make alliances with very questionable political entities, namely the Klingon Empire. I always felt the real core dilemma was swept under the rug in The Undiscovered Country, amid all the rhetoric about not fearing the future. "Let them die" should have been given a lot more serious consideration.
the standard for alliances is often "common interests," not "shared values." The latter is a much higher standard, and might leave the UFP with few allies. That was another silly aspect of INS, the whole "deck stacking" against the Son'a to show that they shouldn't be allies. As you say, the Klingon Empire isn't exactly the most enlightened power, so why are we supposed to frown at an alliance with the Son'a?
And that is an interesting convention that is ignored. The Klingons are a warrior culture that show up, inform the planet that they are now part of the Klingon Empire, enslave the population, take the resources, and call it a day. If the Organian example is any indication of a standard Klingon annexation, it is hardly an equitable relationship between the Klingons and their new aquisition.
But, the writers tended to gloss over that in favor of making the Klingons, at least on the surface, as honor-bound barbarians. It was a facet of Worf that should have been explored: Worf was raised as a human, instilled with human values and culture, even if he was exposed to Klingon ideals as much as possible. Imagine an episode where Worf, who wants to be more Klingon than the archetypical Klingon, has to reconsile his need to be Klingon with his upbringing. The Enterprise shows up to trade with a neutral planet, meanwhile the Klingons show up and simply take the place, do their mass executions and enslavement, and Worf has to decide which is his way: the human, and by extension Federation, ideal of self determination for everyone involved or the Klingon way of might makes right.