You seems to forgot about factions (or i completely misunderstood how they works). If we have some unhappy POPs, we can only deal with them only on Species level. Now, unhappy POPs join a faction. In best case scenario it join some useless faction (or just a faction that directly oppose your policy) you can suppress. But what if it join some useful faction and start spoiling overall Faction happiness? And if i, again, understood the faction system right, a few unhappy POPs could shift overall faction happiness quite a lot.
You definetly did not understand how faction mechanics work in 1.5 (wich is exactly Opposite to how they worked pre 1.5). As "Peko?" explained it to you.
Not to mention that with a single non-fanatic ethos opposing to everything you do, they could never join a majority faction to begin with.
WTH would a Xenophobe in a Fanatic Xenophile empire do in the Xenophile Faction, advocating less Xeno Rights?
And it is not like he could join the Spiritualsit Faction to drag them down. Because he is a Xenophobe, NOT a spiritualist (unless there are overlapping Factions. At least Pacifist and Xenophobe have some indicated overlap).
And that again is before you consider that Faction defines happiness in 1.5. Not the other way around anymore.
I wonder whether given the new focus on the interplay between pops, ethics, and factions, whether it will be possible to change empire ethics in 1.5
While it has not yet been confirmed in a Dev Diary, it was clearly indicated in the
Ethics Rework one and Wiz's Twitter posts, down to screenshoots and discussions of the mechanic.