Im gunna co-op on your idea a bit:

I feel as though the reliance on pausing, as you have stated before, isn't as big of a problem as you would have to believe. Limiting a player to 1x speed on the entire server would be sufficient enough to counteract problems that would arise once a player logs off. These problems would be natural disasters, starvation and plagues of course.

What would be interesting to see is how players would counter act the self terminating style that this game would have once going multiplayer. I mean this as when you leave the game long enough with out doing anything, it will eventually run out of resources and destroy itself. This would be interesting to see players come up with methods of creating self-preserving society that look after themselves when the player is away.

With any add-on it usually creates a new challenge to the existing game. Multiplayer would just be a new challenge to over come for the player. There is a problem however with how resources are shared in the game. The server would have to differentiate between which players resources are being carried by which person. Which in retrospect could be solved by creating a tag as in "Citizen of [X]". Where the player could only then have his citizens interact with his own buildings with a similar tag. Resource accumulation would be solved this way to. Where as any person can pick up a dropped resource, but then can only deposit it within a stockpile in their own land.

Land Sharing would have to be an additional add-on. We couldent have people running into eachother, or destroying others buildings. Rather we could set up a system of land purchase. Where you could by sectors of land and only develop on the land that is bought. This would bring up the question of the ability to expand after such time as passed where your running up against boarders on all four sides of your town... You could solve this with the ability to add an army, or a minuteman battalion. You could preform a hostile take over their city/town with the intent of destroying their city hall or equivalent, giving you their lands and resources.

In conclusion, the pace of play could always be running at 1x speed or lower to allow players enough time to act on significant events. The ability to add a new layer to the pre-existing game's challenges is created, thus adding a unique puzzle to figure out. Lastly, Army's are a good idea.