Huh... didn't even think of maps being copyrighted, but apparently it's a big business. Some manufacturers even have copyright traps in their maps, adding towns or points of interest on their maps that don't actually exist to make it easier to tell if the map is theirs or not.
But here's the trick in this case. Sounds like this guy didn't publish or distribute the map they used, he just did it for S&Gs to show what was wrong. Naughty Dog basically found a way to use a non-copyright map, which is pretty rare, and now this guy doesn't have a leg to stand on in the conversation. Posting an edited map on your blog doesn't make it copyrighted.
Sure it's a bit conniving on Naughty Dog's end, but this guy isn't a victim either. Hell, he just got free publicity for a map edit he's received ZERO money for... past, present and future. Take the publicity and shut up, dude.