1. The Baku planet and system ARE within Federation territory
So? Just because a system is in Fed territory means it's rights are forfeit to the Federation? That sounds like imperialism to me. Last I heard you had to apply for membership to the Federation, you couldn't just be consumed by it. And if Baku was a member planet you wouldn't be able to invade it like that, would you?
2. The PD doesn't apply at all to the Baku, who aren't pre-contact, pre-warp, from that planet, or even much of a "culture" at all-they're more like an artificial little village
(I know TNG really screwed up the PD and made it basically made it mean "the PD is whatever the writers say it is this week," but under NO interpretation of the PD does the Baku situation apply )
You have a fundamental misunderstanding of the PD. It merely states that all cultures have rights and the Federation will not interfere with them. It says nothing about pre or post warp. The Enterprise left the Klingon Civil War citing the PD. I think the Klingons have warp. Take a look at First Contact (the episode) to see. You may contact a post warp civilization, but if they ask you to leave and never return you have to. And you certainly can't interfere in their internal matters even if they ask you to (The Hunted, Symbiosis).
3. How can you say the Son'a have no right to the planet? They're the same people as the Baku! If you say they have no right to the planet, where do the Baku derive their right to it?
The Sona left. They aren't part of that society anymore. Did the pilgrims have a right to England? And even if there was a dispute as to whether the Sona did have a claim that is - again - an internal matter and up to them to figure out. The Feds don't take sides.
4. Are your propertarian principles so absolutist that even when a much greater good can come from a relocation, it's still wrong? If there were a cure for cancer located in the soil of a tiny region and the inhabitants of a small village would have to be moved to get at the cure, would you really defend their property rights over the lives such a cure would save?
Propertarian? You've been reading too much Leguin. It's stuff like this that gives communism a bad name. You can't just take what you want from people because of the "greater good". China, Cambodia, Russia, and even the US all did that with devastating results. Also, just because your system is better than the other guys doesn't mean you have the right to inflict it on them. That's imperialism. But if you think blood for oil is a good exchange then congrats, I guess.
the "dilemma" in INS basically comes down to property vs. saving lives.(the Baku didn't have to die when being moved, they could have benefited from a distance just like others)
This is actually not even the dilemma. No one is really dying en masse in the federation. Its a disease free utopia. The medical tech is perfectly fine as it is. There's no immediacy here that requires forced relocation. There's plenty of time for negotiations, figuring out a noninvasive way of collecting the unobtanium, and compensating the Baku for the privilege.
And obviously the Federation respects propertarianism, otherwise they wouldn't have been bidding on the Barzan wormhole in The Price. You've got no legs to stand on here. You're not being an egalitarian, you're being a neocon.