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.
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?