This guy is an employee of a city that has just had a terrible time dealing with "Southern heritage" issues. He wrote an article over his title as a city employee without the permission of his boss, reigniting the very issues that the city had finally managed to put a lid on.
He certainly is free to say anything he wants, but not to use his city title to give some sort of imprimatur to his speech. And by doing that without permission, he has put himself in a bit of a jam from an employment standpoint.
"Free speech" doesn't mean "speech without consequences", especially when you do something without permission that harms your employer.