The problem is that Stellaris conflates two distinct concepts from Alpha Centauri:
1. Nerve Stapling: Removing higher brain functions from pops; Punishment for unruly pops; works much more through terror than the physical effect on those who are actually nerve stapled; atrocity
2. Genejack: A genetically designed being without higher brain functions; optimized for work; no atrocity
It's kind of ambiguous what procedure genemodding is supposed to represent in Stellaris. (Similar ethical concerns apply to the "uploading" of synth assimilation.)
It could be some sort of in vitro editing of the next generation, Gattaca-style, which wouldn't necessarily count as an atrocity; the old non-modded pops simply die of old age. However, if that's the story, it happens suspiciously quickly. Also, it's still arguably genocide even if no individual pop is harmed, for the same reason that the Neutering purge is genocide.
If instead it's live gene therapy, applied to existing pops, then it's no more ethical Alpha Centauri's nerve stapling. It's a high-tech lobotomy, done by injecting a virus or something instead of brain surgery, but you are still lobotomizing existing sapient pops. (Incidentally, the science to enable this sort of live gene surgery has advanced dramatically *in the time since Gattaca and Sid Meier's Alpha Centauri were released*, particularly since the development of CRISPR gene editing.)
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