Your argument seems to be that an inhabiated world if it falls within Federation space is it's do with as it pleases. So lets take a the Malcorains from TNG's "First Contact". The Federtion could go in transport it's inhabitants to another planet so they cold strip mine that planet. At what number does it becmoe wrong to move people who have evloved/settled there, 1000, 10 000, 100 000 a million?
One, settling someplace and evolving there are two distinctly different things. Had the Ba'ku evolved there and were somehow inextricably connected to the planet then you have a different ball game. Not being inextricably connected to the planet, they simply return to their normal lifespan.
Two, it's not about right or wrong it's about the greater good and it's about logistics. It's about costs vs. benefit. The Federation would reap a massive benefit for a small cost.
Would I have handled the relocation differently? Sure, I've said that on numerous occasions. Would I have relocated the Ba'ku? In a heartbeat. Because the only negative impact is that the Ba'ku returning to their normal lifespan.
If they personally wanted a say in their own affairs, they should've poked their collective heads up out of Amishville and took part in the galactic community.
Your argument is essentially that "might makes right." The planet is in Federation space, the Ba'ku can't do anything to stop from being relocated, so the Federation can just do whatever they want with those people, even though the Ba'ku settled that planet before the Federation existed, and have no reason to respect the Federation's jurisdiction or authority. Whether they evolved on that planet is totally irrelevant. Just because a people migrated from one place to another doesn't mean they have no claim to the land they've settled, especially if they settled it well before anyone else did.
Essentially, the Federation is supposed to hold the sovereignty of individuals and cultures in the highest esteem, but is willing to throw that out the window on a raft of technicalities to get something it wants.
As others have said, the TNG-era Prime Directive does
apply in the sense of not interfering in non-Federation cultures without their consent.
Had the So'na shown up and started ransacking the place or even massacring the Ba'ku, the Federation would have had a justification for a humanitarian intervention, but getting involved with the whole "Fountain of Youth" business is not something they should have ever
entertained as long as the planet was populated, or at least until the Ba'ku opened negotiations on the matter themselves.
Displacing people who've done nothing wrong, who aren't even under the jurisdiction of your government, and saying it's for the "greater good" is quite unseemly.