If you kill an enemy in a sphere of influence, you lose/gain alignment. If you kill an enemy while not in the sphere of influence, you only lose alignment. Why do you lose High Elves alignment if you kill a high elf at the tip of the Horn of Harad? Simple Solution: Similar to killing enemies, killing NPCs of a faction outside said faction’s alignment sphere would make you not lose alignment.
Even maybe a new area, around the basic one, in which killing faction NPCs would still make you losing alignement but killing ennemies won't give you alignements. Meaning you need to be fully out of a faction's lands to kill people.