It would be nice to have an extra field in the table that nodes are stored in that allows admins to override or determine whether the node shows up in the quick nav list. Right now you can determine whether all subforums appear in quick nav, but what if you don't want all subforums to appear? Too many makes the list unwieldy, IMHO, and people won't even read it.
The field could be set when editing a node and there would need to be an edit in the quick_navigation_menu template to check the field before including the node in the right hand column of the quick nav list.
It seems like it would be simple for you XF mod gods out there, but it's beyond my Ken.