Oh, for the love of Pete (whoops, I'm sorry -- Elsa. Look at me, being antifeminist right from the beginning)! Not all conventions are created strictly to keep someone down. If people referred to the city as a man, some people would be just as angry and arguing the issue from the other side -- she's nurtuing! She's a mother! Why do people insist on stripping the city of her power? Etc., etc.

Also, the OP mentioned how jarring it was that she read anthropomorphizing of the city but never saw it on the show. I remember quite clearly John calling her "old girl" last season. Clearly, it's all his fault. John is The Man.