I can't wield my own pillaged weapons, and the guard type mobs in the clan all attack me on sight, even though I am Chieftain.

An Orc that becomes non-evil is automatically a betrayer; betrayers are cast out of the Clan. Since you remain Chief, I have made the guards recognize a Chief that is a betrayer.

Pillaged weapons have been evil only weapons and probably for good reason (tearing limbs off of the dead and using those limbs as weapons requires a certain level of depravity). I have allowed a neutral Orc to use them, however. Making great use of them may require an alignment shift in the evil direction again.

I've been roleplaying that the guards refused to accept my "new way" of leading the clan, and that was why they were attacking me on sight. Now I get to be all smug and chest poundy and like "That's right bitches! Recognize"!