The barbarians attack. The player with the smallest army controls 2 cities, neither of which is a metropolis. Can they choose which one gets destroyed, or is this chosen at random?
You're right, the rules only state that the player loses one of thier cities but not how to determine which city.
However, the mobile app comes in handy. I created the same conditions as you explained, and this is how they designed the game to handle the situation.
So the player decides which of their cities get pillaged.