...You're right. Partial mental lapse. I suppose the damaged city's defense is null from all the conquering and reconquering, and the defender's contribution is only a couple of melee boat suicide attacks away from being extinguished. So yeah, it's a matter of having a naval presence proportional to the threat. If the city was settled across a lake from an enemy colony, you have to be prepared to defend it. I think this has to be the first thread on the Civ5 and CivBE forums complaining about the AI putting up a fight.