that would make perfect sense
let's take a look at alien missions, though, to see what aliens should score points for:
Alien Research - should score points based on percentage, even if disturbed and xcom ground mission is won, I think. after all, they are researching something, and will probably transmit their findings as soon as they are made.
Alien Harvest - should score points based on percentage, even if disturbed and xcom ground mission is won, I think. to reflect the amount of damage they have done.
Alien Abduction - just like alien harvest
Alien Infiltration - should only score points once completed, I think. in other cases, the infiltration simply failed, right?
Alien Base - should only score points once completed, I think. in other cases, the aliens failed to establish a base, right? although you might argue that those are usually carried out by several ships, so maybe they will use a common "counter"? catching one of the UFOs would slow them down, but wouldn't stop them
Alien Terror - should not take much time! I think the (empty) UFO should fly away, but dropping some terror units shouldn't take more than five minutes. the UFO's mission is completed as soon as the terror units are dropped off. we might make it a possibility to catch the UFO on the ground with its crew still disembarking, but you'd have to dogfight-standoff-chase the UFO to the destination city. even then, the aliens should score points for the mission, because you have to fight the aliens inside a city, which causes panic and endangers civilians, so the aliens got what they wanted. even if they lose the battle on the ground and lose the UFO, too. still, this might be worth it for the added loot and for avoiding the dangerous air-combat against a terror ship! but you'd need a fast troop transport to catch them on the ground, probably an avenger, though a lightning might work
Alien Retaliation - that's only UFOs looking for your base, right? they won't land anyway. so they should score points for the time they spend searching undisturbed.
Alien Supply - those should definitely score points based on the percentage of time they spent on the ground (and ideally, should have less loot aboard also depending on the time already spent)