I can second this, not to mention spells like Harm or Enervation and Greater Enervation.
Third problem: Several undead, even in Core, are only Mostly Evil (like Mummies and Mummy Lords) or don't have a specific alignment at all, like Ghosts.
My preferred explanation is that Negative Energy is merely an alternate élan vital, life essence, an equal and opposite to positive energy, like matter and antimatter.