Yeah, there's a bug in the webui connection-manager for close-daemon, but the one in GTK-UI I just tested working, both here in latest v2.0.5, and also checked v2.0.3, as per this thread's title, on an ubuntu VM, so there's that. Alternatively can use the consoleUI which features a 'halt' command, so 'deluge-console halt' cleanly stops the daemon. A small python client script can be made to stop daemon also, but why bother when deluge-console etc works. Only thing not stopable, is the webUI - I thought I remembered an web-API function read about in API-docs, and did mess with it through curl as wanted post a script cleanly closing it(just for others possibly interessted), but for one, there's a bug, as per the webUI stop-daemon bug, as using same API-call regardless, and second, I see it is for killing deluged actually, not deluge-web, just the name in API 'web.stop_daemon', confused me initially. Anyway, that doesn't have a stop command anywhere, but also isn't an issue killing, as just webserver interface for deuged, so I just run 'pkill deluge-web' for that, without issue.
You could always run through a service of-course, like default systemd-service files shipped with the install package, so you can stop/start/restart at will through systemctl/service-manager.
Little longer than I anticipated, for such question, sorry for wordyness
