"--no-desktop
Do not manage the desktop -- ignore the preference set in the
preferences dialog." - http://linux.die.net/man/1/nautilus
So likely you can disable it by it's preferences, but at least by
launching nautilus with the --no-desktop option.
You could edit the desktop file in /usr/share/applications/.
For Caja and Nemo it's the same, while for other file managers it
usually is vice versa, e.g.
[rocketmouse@archlinux ~]$ spacefm --help | grep desk
--desktop Launch desktop manager daemon
--desktop-pref Show desktop settings
--set-wallpaper Set desktop wallpaper to FILE
--no-desktop No function - for compatibility only
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