Comment 4 for bug 204413

You need to remove Nautilus from the session manager first. There are two ways: the easy way is typing 'nautilus -q' into a terminal. The GUI way is by going to System->Preferences->Sessions, switching over to the Current Sessions tab, finding Nautilus and removing it from the session. After this, Nautilus kill be able to be killed without automatically restarting itself via killall nautilus (or xkill, or whatever).

To prevent Nautilus from reregistering with the session manager, you can use 'nautilus --sm-disable'.