Obviously I have no knowledge of how the game works, but I had an idea like this:
Every registered player gets some sort of extra flag, which they have to put in their property within (let's say about) two months, and after those two months, all properties that don't have the flag (there should be some way to do automatically find all flags to make this work though, like a beacon that sends a signal) get deleted.
If the player turns out to be inactive for a couple of months, there's still a big chance his buildings and stuff are still out there, so all he'll have to do is put down his stronghold again.
And worry about having it stolen and griefed :3... we need a new work for Mythruna... He'll be Mythed!
Anyway, not a bad idea, but what about people that are FOR SURE super active? Perhaps an option for admins to do:
PlayerA = NoStrongholdDestruction
Player1 = NoStrongholdDestruction
Teknonick = NoStrongholdDestruction
Paul = NoStrongholdDestruction
RandomDude18542 = YesStrongholdDestruction
AKA, everyone EXCEPT that last guy doesn't have to worry about the auto-decay :3