We don't know which came first, ST:INS or Season 7 of DS9.
IMHO, the movie only makes sense if it takes place after the war. Neither our heroes nor our villains would have any business behaving like that if the war was still on...
We should probably argue that there were three parts to the species there: the original culture from which the Ba'ku escaped to found their paradise planet, then the Ba'ku on that planet, and then the Son'a who split away from the Ba'ku because of reason X. It would be interesting to know what happened to that original culture. Was it destroyed by the forces the Ba'ku wanted to escape? Or did it survive - and if so, did the banished Son'a go back to that mother culture, or did they form their own enclave?
The Son'a seemed to be tech wizards, capable of outperforming the brightest minds of Federation R&D. That might allow even a very small number of them (a splinter group of the original, mere hundreds of, Ba'ku) to enslave the inhabitants of two planets and to build a power base from which to plot revenge.
One could also argue that the banished Son'a went back to the Ba'ku place of origin, a place reputed to be saturated with evil technologies that the Ba'ku wanted no part of. Such a place would be a likely candidate for enslaving the Ellora and the Tarlac. But would Rua'fo represent them all, or only a faction of them? Would the entire original culture move to the Ba'ku planet after the movie, then?
I rather prefer the idea that the original Ba'ku/Son'a home was somewhere very distant, perhaps even in the Gamma Quadrant (explaining how they knew the secrets of Ketracel White), and that there was no going back to that world. The distress of the banished Son'a would then be all the more acute, their plot of revenge all the more logical and lacking in alternatives.
One also wonders how the Ba'ku banished the Son'a in the first place. I mean, if the former didn't believe in guns and violence, and the latter did, how could the former be the banishers of the latter? Perhaps the Son'a were cast out without weaponry, in a rickety starship (perhaps the one, or one of those, that brought them to the Ba'ku planet originally), and spent centuries trying to build up an arsenal. And in the meantime, the UFP claimed the region of space and blocked Son'a access to it...
Lots of possibilities there. Personally, I'd think the Son'a did join the Ba'ku at the conclusion of the movie, and let the Ellora and Tarlac go their merry ways. The ancestral home in turn was too distant to be involved in any way. And the Federation and the Ba'ku together set up spas and hotels to exploit the benefits of the metaphasic rings. Or if the Ba'ku didn't agree, the Federation came and hauled them all away, as per the original plan, and neglected to tell Picard.
Timo Saloniemi