Theoretically, if the heroes have been in conflict with said villain for several exchanges, the villain would be able to buy out of a serious compel with one of the small pool of Fate Points built up from the players' previous compels and aspect tags.
I agree - any named villan important enough to the plot should definatly have some fate when they get to the point they're actually interacting with the PCs (by GM fiat if not actually as a result of compells).
Just because they have negative refresh shouldn't necessarily mean they have no fate.
...and conversly anyone not important enough to the plot to have fate should be able to be taken out with a compel (by the GM or otherwise) of an aspect such as "Asleep" when a PC gets to a point of being able to do something like a coup-de-gras.
It need not require a fate from the player - as a GM I would probably just give the result to them, but the underlying mechanic would be a compell of the aspect.
Storywise as a GM I would be wary about doing the reverse to the PCs - When the ninja squat comes for them, I would feel obliged to go after the person with fate first, so they could at least buy off the compell, or more likely give them an alertness against the Ninja's stealth with an invoke against their "asleep" aspect as they maneuver for "in position to give a coup-de-gras" - handily giving them a fate to buy off the compell of that aspect! - They are important to the ploy after all, and the drama is from them escaping the near death experience not succumbing to it