Sacred Weapon (Su):
.... The warpriest can enhance a weapon with any of the following weapon special abilities: brilliant energy, defending, disruption, flaming, frost, keen, and shock.
Disruption: A disruption weapon is the bane of all undead. Any undead creature struck in combat must succeed on a DC 14 Will save or be destroyed. A disruption weapon must be a bludgeoning melee weapon.
So which of these overrides the other? If my sacred weapon is a longsword (i.e. not a bludgeoning weapon) can my warpriest enhance his weapon with the disruption ability?
Neither overrides either.
Keen has a similar issue, because it can only be applied to slashing and piercing weapons.
There is no contradiction. The warpriest has a list of options for abilities they can apply, which includes special abilities that are limited in what they can be applied to.
Disruption can be applied to a sacred weapon, but only one that is of the correct type. Bludgeoning. Just like keen can't be applied to bludgeoning weapons.