The non-interferance is just one aspect of the Prime Directive. If the Ba'ku told the Federation to get lost, then the Federation would have to get lost.
It does not matter if they are indeginious or not, the Ba'ku establsihed what could be described as a colony before the Federation was founded.
The Ba'ku aren't members of the Federation which means their colonies aren't either. So the Federation has no right to just walk in and take what they want.
I'm curious about what your views on the Son'a's claims here are. They basically ARE the Baku, and all they really did was lose a political struggle. Had they come in, removed the Baku themselves, and then sold the particles to the UFP that'd be fine, right?
I mean, all they really need is permission from the UFP to enter their territory in force. Then the UFP can sit back and watch as the Son'a do the removal work.
Based on your views of the Baku claims, can you explain your objections to this reasoning?