I'm running i3-wm under a gnome session in 12.04.
Nautilus is not normally running.
I regularly loop-mount ISO and other filesystem image files, and every time I do this nautilus pops up both a desktop window and a window opened at the new mount point.
Uninstalling nautilus is not an option -- I tried this, but apt reports that dozens of packages depend on it (directly and indirectly).
This question is similar, but only talks about preventing launching on USB stick insertion. I don't want nautilus to run, ever -- removal would be ok with me if it didn't require uninstalling the world.