Traps and more mechanics, we need other ways to 'hurt' or kill players without actual confrontations.
Of course it should remain in the RPG element, based on the stealth and perception based skills on the base amount for said skill and half to 'detect' it at a chance.
If you want a alternative system to the whole key system, maybe add a little extra function to the game's mechanics for door stats.
Levers - Buildable levers that lets you sacrifice a key to open a door one/two ways and is easily destroyed!
Griefers can't really build and connect one because they do not have the keys, the owners can decide to make one side of the gate connected with a lever to make it operational.
Not sure if there needs to be a opposite, a way to bypass this system for those who wants to invade, if the possibility of using a Ram is not possible.
Actually this could be a separate idea or thread later on when someone feels like making one, but things that 'activates' other things, like floor switches, levers, pulleys, etc.
Since you have strongboxes and palisades that operates with locks, do the notion of actual 'lock' items count in the current lores? The stuff you use when you want to chain or lock something that lets you attach the lock to it.

Allow houses to be locked?