I am also struggeling with the issuse. Therefore I reopend the feature request discussion "Duplicate Entries" and quoted your proposal there,
HippyCraig:
http://forums.wolflair.com/showthread.php?t=51586
Currently I use both realms and geographical / cultural regions as level one
containers, depending on the size and boundaries of the area.
For former ownership, areas beeing parts of vanished kingdoms and the like I use
relationships.
As a consequence I put contested places into the container of the party / realm currently controlling it in actuality and add a relationship "also claimed by".
Even though this approach works somehow, imho it also gives away to much information.