The Baku were made aware of what was going on during the developments in the film. I didn't see any of them saying, "Oh...well, if it will help millions of people, sure I'll move."
Yeah, why wouldn't they be willing to talk to someone who was kind of spying on them and was going to kidnap them in their sleep and was still planing to go through with it even after the plan was exposed?

This. And before the film even started the exiled the Son'a to basic death sentences simply because they chose a different way of life.
Honestly it sounds like they just told them that if they wanted to be all technological and stuff here are the keys to the ship go have fun. Not to mention this was after the Son'a tried to take the place over.
hell for all we know they were expecting them to either not care about the immortality aka the freaking trade off for the own interstellar empire, or to come back in a decade or two if they got bored with the whole thing.