Basically: No
Complexly: Kind of
A city can never be 'destroyed' and removed from the map- they are there to stay.
How ever, a Plague can economically, militarily and mortally 'harm' a city. The Plague kills many citizens, who live their hum-drum lives paying taxes into your treasury. Less people means less tax payers which means less money in the long run. I dont know to what extent the plague can cripple trade income however(probably worth a test or 2). Militarily, it can cripple some defenses and remove the healthy citizens that would normally enroll into your legions. Although you only lose a few soldiers in a unit every turn, i find it best to let the plague ravage them then retrain them only when it is gone (or militarily necessary). Mortally, with the plague again killing your citizens it means the growth rate declines and therefore it may take many moons before your city reaches its population pre-plague.
So the plague has many downsides for a city, BUT it will never destroy it entirely.
Those who cannot learn from history are doomed to repeat it- George Santayana
History is a guide to navigation in perilous times. History is who we are and why we are the way we are- David C. McCullough
Wars not make one great- Yoda