It looks to me more like the reporter decided that Scott's refusal to use his real last name was a weird request, not a legitimate security concern for his patients and himself. The reporter just doesn't get it.
It's not like it adds to the story. Every on the internet knows Scott as "Scott Alexander". I didn't even know it wasn't his real last name until today. It just seems so cruel to insist on doing this to Scott when I can't see any good reason to do it.