Just because part of the population had to leave, does not give ANYONE the right to kick out the rest.
It was an internal rift within the Baku that gave birth to the Son'a, true, one side lost the argument and left.
We don't know how it went down beyond what was established in dialog, so lets base our judgement on that, rather than "what ifs", or "maybes" or anything else we cannot define.
I would say they BOTH, in general, have a right to live on that world, however, everything in the film establishes that the Son'a started a fight, and were kicked out as punishment by that society.
Starfleet clearly had no say in the internal affairs of either society by its own guidelines and traditions, and the Baku were being kicked out by the Son'a, rather than the Son'a fighting to take back their home.
It evolved from a failed uprising, that may not have been as violent as the Son'a ended up being (we don't know either way, so cannot use that in our deliberations), into a forced eviction of the entire population.
If it was just both sides fighting, without Starfleet's involvement, over wornership of the planet, then the Federation's role, if any, would be peacekeeping and diplomacy for both sides.
That was not the case. It was a clear forced eviction, with no apparent attempt at diplomacy on the part of the Son'a, and no chance to gegotiate, or make amends for the Bak'u.