Right now if you --recursive-unset a path or --unset an empty directory, all the leaf node keys are removed, but the directories stick around.
This request was evaluated by Red Hat Product Management for inclusion in a Red Hat Enterprise Linux major release. Product Management has requested further review of this request by Red Hat Engineering, for potential inclusion in a Red Hat Enterprise Linux Major release. This request is not yet committed for inclusion.
So we're not going to get to this for RHEL 5. I moved this upstream: http://bugzilla.gnome.org/show_bug.cgi?id=383044