The rules aren't going to help you there, really. There've been past discussions of it, and they largely boil down to the coup de grace stuff above, and plain GM fiat. At some point, though, it comes down to realizing that some types of story beats just won't work well in Pathfinder, especially at higher levels.
If you want that moment to have dramatic tension, just stabbing the NPC won't cut it. They need to be doing something grand enough that the PCs can't deal with it. A scroll of Destruction or Disintegrate. Drop them into a a vat of acid. Banish them to another plane. Feed them to a pack of werewolves. Anything that doesn't rely on something as mundane as stabbing someone to death.
You'll hit a point where the PCs have the spells and resources they need to raise the dead, at which point most hostage scenarios lose a lot of their tension. Travel will become moot due to teleportation or flight. Long before that, most 'PCs vs. environment' stories are trivialized by Endure Elements and the like. You'll need to up the stakes beyond what would be a threat to normal humans like you and me.