I honestly can't recall whether it's only in the extended version of the film or not, but Sigourney Weaver's character had opened a school to teach the Na'vi English (presumably not unwillingly). My understanding is that originally things between the humans and Na'vi were at least somewhat peaceful, but that matters had deteriorated by the time Jake arrives.
The fact is, if the Baku were willing to let the Son'a settle on the planet, that should have been explicitly stated by someone at some point. The closest I recall the film coming is when Dougherty summarily shoots Picard down saying that for some of the Son'a living on the planet wouldn't help them because they had already deteriorated too much.
I'm not sure it matters whether the Son'a left voluntarily or otherwise, as to me the fact remains that any dispute between them and the Baku is an internal dispute as they're the same people, while humans and Na'vi are not (barring some sort of future plot twist). If the Enterprise showed up in Avatar, and if Pandora was a Federation planet, Picard likely would have sided with the Na'vi. On the other hand, if Pandora is recognized as being in "human (the humans of that universe, that is) space", then Picard's likely violating the PD if he interferes in the affairs of a foreign power.