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.