After thinking about it more, maybe it would be possible just to use some kind of pause timer for the NPCs to start giving zone reset warnings. I still don't know of the best way to reset a zone.
Maybe using a trigger spawn that starts the pause timers as soon as someone enters the zone. Then the zone will reset maybe 8 hours later or up to 24 hours or something.
I wanted to note that there is a thread
here asking for a feature to allow npcs to use GM commands. I think that could open up a fair amount of possibilities for quests.
I don't know if there is some way other servers are dealing with the ghosting issues other than daily reboots, but it would be nice to hear if someone else has found a way to fix it, or good work around for it.