Yeah I've been having the same problems with shifting government ethics. I've angered my pacifists as much as physically possible, even starting a liberation war and just continually bombing the enemy planets for over 20 years nonstop. Planets started actually disappearing due to accidental glassing and I won the war because of it. Guess what? No factions for anybody other than the ones I already had (materialist + pacifist). I executed the pacifists version of exterminatus on a few worlds and my pacifists are totally OK with that. What in the living fuck.
I've been suppressing the pacifist faction for a good 40 years and that has only caused a shift to the pops but absolutely none of the factions. I'm looking at 96% materialist pops, 3% pacifist, 1% militarist AFTER EXTERMINATUS. I've tried a ruler who was war-oriented, a leader who was ant-xeno, etc. Nothing. 40+ years of these rulers who are anti-pacifist. Still two factions. I've had war declared on me, still two factions.
Yet in my game that had insane convergence towards my government ethics - 30% or higher per planet, no unrest, followed exactly what the factions that my govt wanted, I had almost every faction all vying for control of my empire. I'm tempted to put mind control lasers on all my planets just to see if my pacifistic people suddenly become militant isolationists. If that works I'll flip shit.
I have absolutely no idea how to change my government ethos and I desperately want to, as it is my current playthrough goal to do so (go from pacifist to militarist or xenophobe). I've been wanting to reform govt around these ethos, but they won't show up and it's driving me insane.