Now Blizzard is making an entire expansion where they have a character explain all this neutrality.
You can't honestly expect them to just turn their own story upside down and say "What we really should do is make the Alliance and all the races associated with it a faction of pure hatred against the nasty Horde".
It was Metzen's goal in WCIII to make the Orcs not be the stereotypical bad guys. To give them depth and show them as a race searching for identity. The in-game world has to reflect this as a possibility.
Not for story telling quality exactly, but because Blizzard doesn't give enough budget/time to for the writers/quest designers to make parallel factions for every situation(IE, Dalaran for Alliance and Zandalari Trolls for Horde mages, or something).