that's actually a very sensible suggestion, counting civilians inside the skyranger as "saved". would allow for very interesting tactical options: on chryssalid missions, land the transport, secure a small area with high-reaction troops, use psionics to "guide" civilians to the safe zone (as many as possible), take off again...
that being said, it would be really nice if we had some degree of control over civilians. maybe it would be possible to use a civilian-only quasi-mindcontrol mechanic by equipping a soldier with a bullhorn/megaphone?