As you point out the Son'a are the same race as the Ba'ku and thus according to the Prime Directive it is an internal matter of a non-member race and as such according to their own rules the Federation can't get involved.
But the Federation didn't know that until some point during the events of the Prime Directive, the Son'a in part were using the Federation to get revenge.
Again, it's baffling why the Son'a didn't just tell Starfleet the truth and then have Starfleet let the Son'a come in and do ALL the removal work themselves. Forget the observation outpost, etc.
The Son'a by themselves could have just come in and announced "hey, you kicked us out once, we're returning the favor now that we've come back stronger," and just beamed the whole village up. And again, they could have shared the particles that came from the collector with the UFP.
Yet again, showing why INS just doesn't make any sense. It's trapped in its own little world of story logic, and can't bear a moment of logical scrutiny from outside of it.