Yeah, sometimes the faction mechanics are really irritating. Once a faction forms, there is often no legitimate way to get rid of it, and it just seems to grow no matter what "tools" you employ. I normally hate to suggest this, but I recommend just console commanding that crap out when if first crops up. I had a xenophile faction form last week while playing as Fanatic Purifiers ... seriously PDX, wth. So, yeah, that level of nonsense just ruins my fun. And while I hate using console commands, I am grateful that they are there when the devs just utterly fail to provide appropriate tools for empire management. I mean, my FP's would just throw those xeno-loving traitors into a mass-grave with their beloved xenos, but I had no way to do that, so I just hit them with console "social conditioning."
So, as soon as the faction appears:
1) open console and type, debugtooltip
2) look at faciton and see what worlds members of that faction are on
3) find them, find their pop ID # by hovering mouse over pops on population page
4) in console, type: remove_ethic_pop # ethic_"whatever"
(e.g. remove_ethic_pop 2248 ethic_xenophile)
5) then you need to add something: add_ethic_pop # ethic_"whatever"
(e.g. add_ethic_pop 2248 ethic_xenophobe)
If you don't add a new ethic, one will be assigned, and it seems to often (annoyingly) be the one that was just removed, so I find it easier to to just assign a new one immediately and be done
If you do it early when there are only 5 or so pops, it only takes a few minutes. I'm sure it would be a nightmare to try to do now that you have 350 pops, so ... really a management option for future games.
Again, I hate to advocate just consoling that **** out, but ... if it's ruining your fun (as it was for me), sometimes it's better to just remove it quickly and get on with playing the rest of the game in a manner that doesn't feel arbitrarily crapped on by poor mechanics.
To each their own, of course. Just an option for you if you want it.