Ah, whiny, whiny people.
Viz was just following the game convention. In the English version of the games the rival was named Blue, not Green, so they carried this change to the manga translation too, not to confuse ORDINARY fans who know "Blue" solely as the rival from the games.
"Ordinary" people don't know Japanese names at all and aren't even aware that the first games released in Japan were "Red and Green". Viz does their translations to ordinary, everyday Pokefans who just play the games, watch the anime and read the manga, not whiny people who want everything to be exactly as in the Japanese original.
I think that the only thing that confuses people are whiny fans who use Japanese naming for these two characters even when they're using English names for all other characters. Heck, even Bulbapedia used Blue for the girl and Green for the rival until pretty recently.
Yes, it's the FANDOM, not NoA/Viz who made this all so effed up. You must understand that if Viz followed the Japanese version, most people would be even more confused than now.