As reported by a Debian maintainer (http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=673363) it might make sense to not show Thunar desktops file in DE which already have a file manager.
Adding Nick to CC: since Jannis is a bit MIA nowadays
No idea what other distros think about this. We can add OnlyShowIn=XFCE; but that will affect also people who install thunar as an alternative to their current file manager.
Another proposition would be to add NotShowIn=GNOME. In that case, gnome users willing to use would not see it by default, but since they would already need to do some kind of manual tweak to use install it. However, it seems that alacarte hides such entries, which make them really hard to find for a casual user who just want to use Thunar inside GNOME.
In other words, no good way to fix this, because Thunar is also used quite often outside Xfce.