That's not what's wrong with purging at all.
What's wrong with purging is that there is NO UPSIDE to it.
Something bad happens - you lose a pop, and all its associated tile production and growth time - and then everyone hates you for it diplomatically.
Even if 1.5 changes things such that, say, only the home empire of the species you purged cares, that only softens the blow. Purging still remains a net loss that no-one would do unless they were "Shoot themselves in the foot for the RP challenge" playing.
And call me old-fashioned, but I like the mechanics of my videogames to at least theoretically have some competitive utility. Whereas what seems to be happening here is they're adding more options that no-one will ever use in a tight game.
There are some benefits to purging.
You already have multiple slave mineral producing worlds, and need to balance out your science ratio, but no planets are nearby to colonize with your species, and terraforming is slow or unavailable to you, but you have enslaved another species that has at least some positive traits regarding science and or energy production. What you do is take that one pop and place it on one of your colonized worlds, when it reproduces the new pop will have your exact ethos - you then purge the old xenos without your ethos or just colonize on a new world, the original grower pop more than likely still needs to die, and replace with the new pop, and now you have a largely loyal species, who is excellent at science, can be placed in the docile faction eliminating malcontents, and can help you further colonize without your own species particular downfalls, you can mix and match the various species and get the exact trait, and ethos combination far faster than with negative ethics divergence or single planet gene modding which typically comes later in the game.
Further, if you colonize a planet early that is somewhat far away from you, and worse yet has an ethic divergence malus attached you may find yourself having to purge not only the initial pop that diverged but its offspring, with purge say it's 2:1 ratio you can purge a new pop every month until you get the pop with your matching ethos to spawn, and as that pop grows, and the other/s is purged your planet is back to being fully in line with your ethos.
Then there are the horrible planet choices the ai makes, and you being unable to evaluate the planet beforehand decide that the 14 tile planet isn't worth the 24% science increase or over core energy/influence cost to manually redevelop it, and you know if you throw it in a sector as is, it is barely if at all an asset with multiple labs, no power/mineral hub/slave processing, multiple tile blockers, etc.
Mindlessly choosing the cede planet option every time, throwing up a space port, and putting those planets in a sector will take you far in stellaris, but there are slightly better options, and purge occasionally lends itself to that.
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