How to deal with homelander factions?

Solution 1:

I had a similar problem. I vassalized my rowdy neighbor and integrated him doubling the size of my empire. Only problem was they were a bunch of xenophobic slaving ****s. Try this;

1. Click on the rowdy planet and go to the planet summary screen
2. Check out the edicts list.
3. Happiness and Ethics Divergence.

Happiness will decrease the likelihood that pops join a faction. Ethics Divergence will change the traits of their pops over time. Usually towards your main race's traits.

Give it a few years. Keep pumping up happiness. Change government types if it increases happiness or ethics divergence. If all else fails, station an army there and wait for the revolts. When you crush them, they'll shut up for a while.

Hope this helps!