Some people want to live in isolation. It's their choice.
They settled the world as colony before the Federation existed. Even in our own history people have settled in new places for a vareity of reasons.
So the reason why the settled the world is not important, the fact that they did is important.
in what sense does the PD apply? They are not pre-warp, pre-contact, or even native to that planet. Dougherty openly says that it's not a PD issue.
Moreover, even if it WAS a PD issue, then nothing would prevent the Son'a from coming in and removing the Baku, and Picard would be in violation for interfering in a "blood feud."
You can't have it both ways.