Unblinking - I find your criticism a bit baffling, as (taking it entirely literally) the story is clearly about cities having some sort of spirit that is independent from their inhabitants. We can argue as to whether this makes any sense in reference to how cities actually work, but your critique is sort of like saying that a story about a unicorn is unrealistic because horses don't have horns.
My comment's not about realism, it's about suspension of disbelief. Obviously, I don't require my fiction to be provably realistic, or this would be the wrong place to hang out. It's not at all like your example about unicorns--although I don't believe that unicorns exist, I can suspend disbelief in their existence, and so a story about unicorns or dragons or tentacled creatures from the depths is not a problem.
But I don't find it easy to suspend my disbelief for this one. To me, if a city is alive, then the living things within it are the cells and the organs that make up its existence. This metaphor makes a lot of sense to me. But to me, the way it happened in this story, is like going to the doctor for a routine physical and finding out that I'm dead, but that all of my organs are in working condition, and the fact that I'm dead is pretty much irrelevant to my everyday existence. I still go to work, I still eat and sleep and do all the other functions necessary to keep my organs running properly, I still think and feel and love and hate, but I am officially dead. That's pretty much what this story's explanation seemed like and it didn't really make sense to me. Sort of like I also have trouble suspending disbelief in sparkly emo vampires--if vampires exist, then the True Blood vampires make much more sense to me, more predator than human.
So it's not that I find it unrealistic, but that I found that I couldn't suspend disbelief. Which you can interpret as being something about the story, or something about this reader, whichever one is perfectly valid and at least partially true.