The way it was meant was that trespassers will be flagged criminals so you could legally kill them.
Actually... I believe that trespassers are only dinged -1 alignment if caught trespassing, but not flagged criminal.
If we implemented a guild system in YO, which I've wanted for a while, it would be a great solution.
For instance, a mechanic that would flag someone a criminal if they stole an item that 'belonged' to a player of a guild other than their own.
Unless we see a guild system, I think looting 'guild owned items' sitting in the open will be a perpetual problem. As for personal items, these can be stored away in private chests/houses when a permission system is developed, which would ALSO highly benefit by a guild system (as in granting permission to particular people within the roster to have access to certain doors/containers).