and one example in Trek would be the peace treaty with the Cardassians which I strongly approve of. Peace for trillions is more important than the property rights of millions of settlers.
You mean the treaty the Cardassians wasted no time violating and it took a freaking Cardassian to let the federation know about that, and still they only gave a minor token response that didn't really solve anything and pretty much only cracked down on people who probably weren't even their citizens anymore because they didn't like the federation just sticking its head in the sand and ignoring the problem. becuase that kind sounds like a crappy treaty, seeing as the federation didn't seem interested in making sure the Cardassians actually followed its terms.
Of course it wasn't OK that the Cardassians tried to arm their settlers in the demilitarized zone. If I remember correctly the Federation eventually decided to monitor the DMZ better and prevent weapon deployments.
But the people who later partly became Maquis could have simply left their colonies instead of stubbornly persist to continue to live their under Cardassian rule and, big surprise, being bullied by them.
I am firmly on the side of the Federation. Sure, they reacted too late to the Cardassian misdeeds in the DMZ but the Maquis did something far worse, they threatened the hard-earned peace and made it much harder for the Feds to solve this problem: we know from Jesus, Gandhi and Martin Luther King that sometimes the best way to defend yourself is not via picking up arms as this gives your enemy an easy excuse to crush you.
Don't get me wrong, I understand the colonists. They have chosen a hard life on the border and their life's work is materialized in their colony so they naturally don't wanna leave. But I also gotta pull a Spock here, their interests matters less than maintaining peace ... and while the Feds didn't expect beforehand that the Cardassians would lead a proxy war via arming their settlers they knew perfectly well that living under Cardassian rule will be nasty for those of their settlers who decide to stay.