One of the department stores in Rochester, NY (where I had my first job after getting my law degree), McCurdy's, had a lunch counter like the one you described. This was in 1979-81; I have no idea whether it still does or not, or whether the store still exists.
Sadly, not only is McCurdy's gone but most of downtown Rochester is now empty. Last year they tore down Midtown Plaza (one of the first indoor malls in the US) to put up office buildings.
And in fact as far as I know, they tore it down for nothing, the office building in question never got built and last time I checked, it was a big stinking hole in the ground. And you are right, it was one of the first indoor malls in the US, and I think the first one that was built "downtown" in any city in America.
I used to visit Rochester to see family. Christmas-time was great, I remember the windows at McCurdy's and Sibley's, rival stores, across the street from one another.
I remember the Santa Mountain and the Monorail inside Midtown Plaza and the Clock of the World (or whatever that clock was called).
And I do remember the old lunch counter at McCurdy's, though by the time I had a job in downtown Rochester it has been moved into the plaza. And the plaza was already majorly downhill, lots of kids looking for entertainment or trouble or both wandered through it, making noise,. It was the hub where all buses met, and the school kids rode the city buses I guess.
Also I remember the Top of the Plaza restaurant was considered a fancy type place to go for lunch, when I was a kid and we were visiting, we got to go once, which was about our only occasion to ever go anywhere considered even slightly fancy, since we were poor at the time.
Anyhow thanks for bringing up the old McCurdy's, brings back some memories from several times in my life.