This all makes sense. And it works for heroes vs orcs.alignment is a mechanism to legitimise player action. You're not meant to question the validity of the labels...
The moment you do, you get the kind of problems you outline - viking clans that have no real claim to the moral high ground being given a moral label. Or samurai - that in their own eyes would probably see themselves as good - being labelled evil to legitimise the players slaughtering them.
Alignment is a design which allows dark ages freebooters or medieval warriors some simple moral certainties when they are being played by 20th century Winsconsin insurance underwriters. The game isn't really set up to challenge those certainties, just to legitimise the resulting killing and looting.
So I guess maybe my OP is really a type of lament - why hamstring the potentially interesting situations these modules offer by bringing in the needless alignment mechanics? It's like a deliberate refusal to present your work as the best it could be.