I was just about to go on an HP tangent
rant about some of the fundamental problems of that world...but I can be distracted from that.
Now, to be fair on this front...Areru has not regained any such abilities, and Alchemist has not used them. Soul
damage, yes, but even that was mostly on non-sapient monsters or a by-product of other factors (like the Dragon-born have Eldritch draco soul cancer). And frankly, even then soul damage isn't much used for actual combat.
Outright destruction of a soul is an ability that Al only gained in the main story when he got an Angel blade (Hazbin Hotel) from Lucifer via his multiversal connections. And he only made that into a weapon in the literal last chapter. His only plans for it, hinted at or shown so far? Are using it on extremely powerful entities that he has no choice but violence (like gods like Zeus, whose Oversoul definitely will NOT be destroyed, though the local version may be damaged or lost), or particularly nasty demons (like Trigon, who was heavily hinted to be the primary victim of the blade according to time-travelers).
Ie, the only soul destruction going around is on targets that
genuinely deserve it...or aren't going to get destroyed.
I guess arguably he destroyed Wotan's soul by trapping them in a universe succumbing to entropy on all levels...but they were also really high up on the 'evil' scale, and it's very indirect.
So this argument is NOT comparable.
Edit: I misread and thought you said soul destruction. For soul damage, there is the thing with Gendo...but that's frankly the only viable comparison I see here (might also be the only time he used that skill on something besides a Fog Demon). He rendered judgement for a wrong of some kind, neutralized Gendo's threat to others, and left him in such a state that he could be taken advantage of, most notably by Areru himself. In those ways sanctioned memory removal and targeted soul damage are similar...but the big sticking point is that you can hide the abuse of one by it's very nature. Not so the other.
Edit 2: This is not to say that Areru sill isn't being extremely irrational. He definitely is. He's got no actual evidence that the Kanto Association has been abusing memory modification like that, only the scumminess of the Kansai and his own experience with human nature. He's also not accounting for practical considerations on alternative measures for dealing with people that are trying to break the masquerade besides death, imprisonment, or grievous
bodily violation (polymorphing). This is clearly one of Areru's hot buttons. He's got some valid reasoning for his reaction (and on some level, is probably right just going by statistics, even if institutional corruption is far from guaranteed), and he had a fairly irrational response. He's also a teenager and/or juvenile dragon. Those...are not historically the most logos focused of beings.
...what did I say about not wanting to go on a HP rant?