Star Trek Insurrection is one of the rare films where I ended up supporting the villains. For a film that emphasise on the moral message, it's shows that it failed badly. The movie clearly try to present that Ba'ku were innocent "good guys" being victimised but what was on screen didn't match that intention and in fact I believe that Admiral Leyton and the Son'a were in the right in this film.
Here are the major issues of how the movie messed up
1) Admiral Leyton stated that the Ba'ku planet was in Federation Space.
In fact that was the reason why Son'a was partnering with the Federation in the first place. Like he said, Son'a had the technology and this was on Federation territory and hence a deal was made. It was also established that the Ba'ku weren't native to the planet and settled there.
So isn't this just a case where the Ba'ku are squatters on Federation property and that the Federation are just evicting them from their own planet that they already own? Therefore this is just the case of eminent domain.
Now clearly this is just a case of bad writing and I don't think the writers intended this to come out this way. What the writers probably intended that the Ba'ku settled the planet first but the Son'a has to cross Federation territory to reach the planet. In fact when point out this fact, people try and defend the movie and say that the time period the Ba'ku settled the planet predated the birth of The Federation. However considering that you have to used Star Trek canon to work that out, for the general audience who are treating this as a film in its own merit the only thing they heard was that this planet was in Federation space and hence Federation property. An average audience would not know whether the Ba'ku settlement predated the Federation. Either way it's just bad writing.
However even if I handwave that line and pretended that line didn't exist and that the Ba'ku do have legitimate claim to the planet this is still problematic because...
2) The Son'a has equal claim to the planet as the Ba'ku
One of the "twist" from the movie was that the Son'a and Ba'ku are the same race. However one side wanted to use technology and the other side wanted to abandon it, the anti-technology side won the conflict (which is actually quite bizarre when you think about it) and then exile them from the planet. However both side has equal territorial claim, it's just Ba'ku won the conflict.
So here is the thing, Son'a and the Ba'ku both have legitimate territorial claims to the planet. One side the Son'a wants to share the planet natural healing properties to the rest of the galaxy. The Ba'ku wants to horde it themselves. How on earth are the Son'a villains in that?
The only time where the Son'a step over the line (considering that they were using non-lethal weapons beforehand which is quite strange for the "villains" of the film) was when they want to destroy the planet with the Ba'ku on it but that wouldn't have happen if Picard didn't interfere and resisted the recolonisation efforts.
The movie wanted this to portray it as a case of colonialism where Federation stealing and exploiting natural resources from the original inhabitants of the planet. However what this really is Federation taking a side in a civil war. Now this definitely breaks the prime directive as Federation is intervening in a "internal conflict" of a civilization but this is certainly not an invasion.
Hell I don't really believe in the prime directive so I don't believe that the fact that Admiral Leyton picking sides in a civil war is a bad thing. However even if you think that breaking the prime directive is a bad thing in of itself, this is not a black and white Federation invading the Ba'ku and stealing their natural resources. The situation is more nuance than what the message of the movie is trying to portray.
3) The Ba'ku were probably the villains in the civil war with the Son'a
Now from my personal views, I would be the person in the pro-technology camp and hence I'm not particularly sympathetic to the Ba'ku ideology but not only that when the Ba'ku won, instead of realising that PLANETS ARE BIG (you know there are 7 billion people living on earth) and have the Son'a lived in the opposite side of the planet in their own separate communities. Instead they wanted to horde the entire planet on their own despite a population of a few hundred people living in a very small community in one small village. They want an entire planet to themselves and couldn't accept that a community with different ideology could share the planet with them. To me it seems like the Ba'ku were being huge dicks in their civil war and being huge dicks when they won the conflict.
My only conclusion is that Admiral Leyton and the Son'a are in the right. The Son'a wants the planet resources that they have as much territorial claim to and share it with the Federation while the Ba'ku wanted it to keep it for themselves.
The thing is this could have easily be solve. Keep the original premise of the of movie. Michael Piller wrote the script and apparently the original draft was that the Federation and Romulans allying themselves to take the natural resources of the Ba'ku who were indigenous to the planet. The idea of this small group of people vs two superpowers. I have no idea why they changed that from the original concept
If the Ba'ku were indigenous to the planet (instead of the stupid this was in Federation space) and the Son'a were removed from the story and replaced with the Romulans and hence we wouldn't have any problems of civil war complicating the issue. This would clearly be a black and white superpowers ganging up on a minor civilization for natural resources that the message of the movie wanted to portray.