The reason that's a terrible example to try pulling is that the USA was so paranoid they interred the whole Japanese-American population... none of whom had done or went on to do anything questionable in support of Japan. The fear was entirely baseless. That assimilated population wasn't suddenly up in arms at the war against Japan.
Actually did Japan ever release documents about the spy atempts on US soil during WW2? It was unjust, no doubt. But I also do not put it beyond them to having had spies there. It was a important part of how you did warfare back then. Especially if they read "The Art of War" from Sunzi.
And to get back to your conquest of the rest example: The last thing you want as a conqueror is unrest. The best way to foster unrest, is to treat people worse then thier brothers and worse then thier previous lords.
If you want them to suffer, it is only natural that the already integrated people would be pissed about that as well. Wich just lowering the living standarts for the entire species perfectly simulates.
Just replace the action you are taking agianst them. What if you were purging and food processing those new conquered pops instead of enslaving them all? How would the ones already integrated NOT be pissed about that? Same effect, different severity.
If nothing else, the already integrated pops will fear "being next". Because why would they not?