Mindwipe, servitor-ed, or BLAM. I personally like the idea I read a while ago that the Inquisition says, "Everyone died - discussion's over", then takes the survivors and makes them Inquisitorial troops (after screening). So they're not dead, they're just serving on a farm upstate.
The latter half of your comment is exactly the basis for the All Guardsman Party. It makes a ton of sense - you need people to do dirty deeds, you also need to disappear a bunch of guardsman, problem solved. Same as using convicts in Darktide.
Problem is that it makes too much sense for 40k. It's gotta stay grimdark, doncha know? Also it's directly in contradiction to lore from e.g. the conflict between the Space Wolves and the Inquisition.
I've always thought they should just start splitting the setting into more and less crazy versions. Or (gasp) do human factions that aren't the Imperium. But that's just my nonsense.
I mean, the place is so absurdly big and spans so much time there's room for variances in procedure and tradition, even inside the same organizations. Especially the inquisition which seems to grant its members an unusual degree of autonomy (from the few books I've read that featured them). But even the guard fields a wide variety of regiments with different specializations and ways of doing things. I just sort of assume the mechanicus and administratum and others all see a fair bit of variety, if only because the empire is so huge and poorly coordinated. The variety of tones in different stories is also something I like, for some reason - it seems to help show the scale, I think?