And why is that a bad thing? Alignment sounds like a declaration of intent...nothing more. I see no real purpose behind alignment in terms of game mechanics and certainly hope none are made a hardcoded part of the game. The glory of a sandbox game is that those playing in the sand get to make up the rules concerning their interactions with each other.
My tribe, the Sac and Fox, may be a good aligned guild...but my neighbor, the Iroquois Confederacy (also a good aligned guild) has been hording all the trash dumps and wont give me permission to cross their land to get to that prime fishing hole. I have meditated long on the subject and sought guidance from my spirit totem...the great bear came to me in a peyote induced dream and showed me the path...the Iroquois must be forcibly removed for the good of my tribe...it is a moral imperative. Nothing in the game should prevent me from warring with like-aligned tribes...or from creating temporary alliances with dissimilar aligned tribes (the enemy of my enemy being my friend after all).