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.