I have just read this discussion, and I'm very sad that it is over.
My 2 cents on this issue is that for me, civilians running towards the Skyranger once in sight, and even running in and using up space, or just generally obstructing the way of the X-Com would be annoying, but realistic, and therefore I'd deal with it better than the civilian, who runs out from below the Skyranger towards the aliens.
Did all effort cease for modelling a more complex civilian behavior for the vanilla game (with an advanced option switch of course)?