Bomb them - system upgrades will get destroyed, pops will get killed, they will stop being able to sustain population.

Hm, they might be a fair number of reason. Can you upload a save ? Seems an intersting challenge.

There is the save, it's the last Riftborn planet at the top of the map. 

So just for refrence I play a custom nation and the orange empire was about to attack me, but I offered them peace. Also, I changed the maximum number of colonized systems before discontent so if you don't want the empire to explode in one turn, you might want to use a mod.

Also, I don't have siege ships at the time of the save, but I have all the ressource to create and produce them in one turn.

I know that I can bomb them until they all die, but I prefer to avoid bombing the system for 15 turns. Harmoneania New Path 19.sav

Hello. Well i charged the game without the mod. Every thing was at rebellion because of that i guess. I only had to attack the system and use preventive bombardment two time to capture it. Maybe the problem come from the mod ?