The nitty-gritty of Shadowrun's version is actually pretty good - it's not actually the soul that is harmed by augmentation, it's "the ability of the soul to recognise its material-plane anchor". Thus most purely restorative things like cloned limbs or corrective surgery, and such don't have an Essence cost (or it's minimal), as there's no sudden disjoint - the astral form was always that way, or organically changes at a rate it can follow.

Essence loss has no real effect on characters IIRC (some effects on getting magic to work on you, maybe a bit of social stuff but with the same "probably the social phenomena of being a walking killing machine, and forgetting to turn off your Wired Reflexes in public" rather than soul damage), until the point that your astral form no longer recognises your body and falls off. This isn't presented morally, it's just a metaphysical phenomenon that can be understood in-setting and therefore addressed.

Advanced tech and magic was slowly beginning to understand how to create augmentations that respected this - geneware, symbiotes, nanotech, to begin with - and had even begun to work on a way to restore that connection (via using the Metahuman Vampiric Virus, which is capable of Essence restoration somehow).

The only real EEEEVIL cyberpsychosis was from the Cyberzombies, a crude and classically corporate black project on "we wanna make supersoldiers but they die if we stuff too many guns in their skull" where they "solve" the problem by getting Blood Mages to staple their dissolving astral form back into their should-be-corpse and add Forced Memory Stimulators to try and constantly trick them into thinking they're alive in between killing sprees. It's pretty fucked.

But I stopped caring about keeping up with Shadowrun with 4E (because of the embezzlement from writers, and subsequent scab takeover of the setting), so who knows how they present it nowadays...