kdebase generates a link /usr/share/applnk/gnome which points to /usr/share/gnome/apps. However, if you install a KDE workstation without GNOME, you get a broken link. Doesn't look too good ... maybe include this link in a gnome package?
Gnome packages shouldn't create KDE's directory structure either... There's no really nice way to handle this. Using rpm triggers could create the directory when it's needed, but it would cause a mess because no package owns it (and therefore, it won't disappear on rpm -e)