After a user logs out I can still see various processes running belonging to that user (e.g.
launchd). One of the resulting problems is that I can’t edit such a user in the System Preferences > Users & Groups since he appears to be logged-in…
How can I completely log out such a user (without violently killing his processes)?
Alternatively, could the user himself logout in some different way so as to not leave such a state?
Don’t use fast user switching: it doesn’t actually log the user out. If you fast user switched because the user left their screen locked, note that as a system administrator you can unlock it with your username and password, and then log them out normally.