I remember a long time ago a discussion about an alternative way to handle weapon proficiency in A/D&D. The idea was any class could use any weapon, but the damage dice of the weapon was tied to the user, not the weapon. So a fighter, a thief and a magic user could all use a longsword, but the fighter did d8 with the weapon (he is a master of weapons), the thief a d6 (some training, but not an expert) and a magic-user a d4 (he can swing it around and hurt someone, but isn't nearly as good as the fighter or thief.
That was considered a viable mechanical option at the time. Same longsword, different damage depending on who was using it. If that was an acceptable mechanic then, I fail to see why a PC and NPC doing different damage is unacceptable now.