IMO, if the PCs interrupted the Villain or directly prevented him from accomplishing one of this goals (or a step towards one of his goals), then the party gets "Defeated/killed XP". If the Villain wasn't totally set back, but just had to run to figure out another plan or because he didn't want to press the fight right then, give half XP.
If the villain managed to accomplish his goal in that scene, and then got chased away, give a token "you role-played a scene" award.
I've stopped running XP as a one time goal (when you 'kill' the NPC). If the PCs can beat the Villain in a social contest, and disrupt the villains plans, they get full XP for "Defeating" the villain, but he's still out there, and will probably be back. So they can earn XP for each time they "Defeat" the villain, and probably a bonus for when they finally Kill him.