those are not options :p
What it currently does is that it just is a missing alien, not counted in the debriefing score. Which I think is what happens too if you do this in the original game.
An alien or soldier under mind control when game ends, those are counted as missing, no matter where they are.
What could be an option is that a check is done if there are (mindcontrolled or not) aliens inside your craft and you are not allowed to take-off before you killed/stunned the alien.