I think the best (easy) solution would be similar to what many people are saying. Most creatures would kill population and destroy some buildings while only the really large ones, like dragons, would destroy the entire city outright. Basically, the stronger the creature, the more damage done.
However, what I'd really like to see is a little more variety.
Animals and other less intelligent creatures would act more instinctively and, basically, leave the player alone in most cases. There's really no reason a bear should be going in to attack a city.
More aggressive creatures, though, should be more aggressive and attack the player / AI more often. This is especially true if, say, the player builds near their lair. These types of creatures would then be much more likely to come attack.
Finally, more intelligent creatures may come attack and attempt to capture cities. They would then build up forces and try to capture other nearby cities.
I think something like this would change the dynamic a bit and make for a more interesting game.