I have KDE installed in Ubuntu (not Kubuntu) and the Nautilus starts with it.
But it should start only in GNOME or Unity:
$ grep OnlyShowIn /etc/xdg/autostart/nautilus-autostart.desktop
OnlyShowIn=GNOME;Unity;
Uninstalling Nautilus or saving the KDE session is not an option. It should not start at all.

#!/bin/sh. Then it will "not start at all". – BlaXpirit Jul 25 '12 at 19:56