Hi,
I have never had any desire to abandon a city in any of my games, but if ever the situation did arise I would do the following: open up the game editor and simply delete the city.
This, of course, could only fairly be performed in a single player game. Logically, a city could be abandoned if the cost of maintaining (or rebuilding, upgrading, etc) exceeded the value that could be extracted from the city.
I think this is a fair and valid move when playing single player. For multiplayer situations, terms would have to be agreed upon before the game. Ultimately, I do not think it will make that big of an impact on any game.
One only has to look at recent history to see examples of a possible city abandonment: New Orleans, places that have been struck by earthquakes, old time western cities in USA that are only small tourist spots without a population, but were once thriving mining towns, etc. [note: this last part concerning New Orleans I am not entirely sure of, but I heard there was talk of not rebuilding it... I do not know where the citizenry and gov't stand on this issue today.]