It only makes no sense if you don't believe governments should stand by any principles.
If the Federation wanted to do only what what sensible, well, for starters, they'd have nuked that pesky Bajoran wormhole once it became clear the Gamma Quadrant was occupied by a ruthless, expansionist force bent on conquering what was on the Alpha Quadrant side of the wormhole. Sometimes you make decisions based on their more far-reaching implications, rather than what looks to suit your own best interests right this second.
That you think the Son'a are more worthwhile allies to the Federation is odd, to say the least. These are people who manufacture drugs for the Dominion, use outlawed subspace weapons, and conquered and enslaved two other species to serve them. If the Federation cares about its image at all, they wouldn't be caught dead trying to make allies out of such people.
There may be no strategic advantage to being friendly with the Ba'ku, but at least the Ba'ku aren't complete bastards.
you're reasoning as if siding with the Baku is by definition the ethical thing to do, and the only reason to side against them is for realpolitik reasons.
Now you're getting it!
That's why the question becomes, "Does the Federation have the right to do what they please with the Ba'ku planet, the rings surrounding it, and the people on it?" The Ba'ku were there first. Homesteading is a pretty old legal concept, one that the Federation (presumably) understands and respects. That the planet is in Federation space shouldn't matter that much, since the Ba'ku were there before the Federation even existed. The Federation just deciding they can uproot the Ba'ku and take the planet's radiation without so much as a "by your leave" doesn't strike me as the action of a benevolent, democratic government. It is the behavior of a bully who is used to taking what he wants by force.
Whether the Ba'ku are from that planet or not doesn't mean much. No one anywhere lives on the exact same land their ancestors did, stretching all the way back to the species' first sentient thought. People migrate, whether it's on the surface of a planet, or to another star system entirely. If you are the first to settle a place, you have a greater right to it than people who show up later saying
they have some claim on it.
So arguing "well, the Federation would help if they wanted to do the right thing" is a non-starter for me. I don't believe stopping the removal of the Baku is the right thing.
The Ba'ku had every right to be there. So did the Son'a, for that matter, since they'd previously lived on the planet. Now, if they can't do so without trying to kill their Ba'ku relatives, that's a problem--one the Federation may or may not want to get involved with. Either way, the Federation has no business
aiding and abetting the Son'a in this--particularly not if the Federation stands to benefit from it. That's just scummy.
As for allies in war, you can't afford to only be allies with those with the highest ethical standards. The Romulans certainly aren't a democratic and progressive ally, and they enslave other groups as well.(like the Remans) I guess the Federation should dump them as allies at the earliest opportunity, right?
When you make alliances with shady scumbags, you know what you get someday? Blowback. Imagine the Federation helped the Son'a relocate the Ba'ku, made them all mortal, took the radiation, doomed the planet, and dumped the Ba'ku off somewhere else. I wouldn't be surprised if a disgruntled Ba'ku showed up on Earth a few years later to blow himself up in the Federation Council chamber. That's what happens when you team up with bullies and despots because it's politically expedient. The little people you step on
get pissed and will come back to murder you for it someday.