I am very sympathetic to this attitude. In political terms it is basically an advocation of a strong, centralized progressive government (as opposed to lefties with slightly anarchic leaning who only play this game of "we gotta keep power in check"; no, we gotta take power) and one example in Trek would be the peace treaty with the Cardassians which I strongly approve of. Peace for trillions is more important than the property rights of millions of settlers.
I now think that the crucial dividing issue is my focus on rules and your focus on outcomes.
If I understand you correctly your point is that the Baku are screwed anyway. The Sona wanna take their planet and if they don't do it the Romulans or Klingons will do it sooner or later. The hippies are simply crushed so even a bad deal with the Federation is better for them.
My point is that the Feds have to play by the book. They are basically a soft power like the EU, not expanding via applying force but via being attractive. If they start to just take planets and rationalize it via correctly saying that the inhabitants are better off than if they had become conquered by the Romulans or Klingons they break their rules and ruin their reputation.
yeah, that sums it up nicely. My view is the Baku are screwed anyway, the Federation might as well benefit from the situation rather than the Son'a alone, or some other power in the quadrant.
I'm a pragmatist and a consequentialist.