The natural disaster idea could be interesting. But why have a single world disaster? It could be an ongoing effect. Hurricanes could randomly move across Beta, obliterating cities they strike dead on, and damaging those struck a glancing blow.
If I really wanted to wipe out cities, I would suggest a Happiness scale for them, and a certain chance of rebellion every hour that the happiness remained below a critical threshold. One of the most unrealistic aspects of the grepolis simulation in my opinion is that your population obeys your every command despite your style of governing. I would have certain events lower happiness. Lopsided losses on the attack, a majority of troops stationed away from home for an extended period, a REALLY lopsided loss on defense, etc. While happiness would gradually recover to 100% when none of these factors are in play.
No longer could players simply stack the cities on the border. They would have to constantly cycle the troops or risk the cities in the heart of their empire rebelling and turning ghost. And more thought would go into the attack. Did city A lose horribly the last time you attacked? Well, let's not use its slinger nuke then. Better attack from somewhere else, even though the transit time is a little longer.
Of course a change like that would probably lengthen the game, making an ultimate victory even more difficult, much to the misguided dismay of certain camps, and much to the relief of those like myself.