How do I disable nautilus desktop?
Install gnome-tweak-tool. There is a setting called "Have file manager handle the desktop" that you can switch off.
The configuration system has been replaced, so gconf won't work in all cases anymore. However, not all apps have been converted yet, so it's still present.
For gsettings based desktop environments (such as those that use the openbox window manager, as Shailesh has pointed out), the following gsettings corresponds to your gconftool-2 invocation:
gsettings set org.gnome.desktop.background show-desktop-icons false