In some of the games I have played, Yes one or two Civi's, get mind controlled, but that is limited to how many Physic-Amps the aliens have, which would and could not be all of them at once, and for shear panic you would get a couple more, but you would think that they would make there way to the path of lest resistance, and not into the Danger Zone! Some times you could get the John Wayne type, that would, if armed take on the aliens, but how many are there in the general population, a hand full at best.
As a distraction to the game, they do get in the way, which is all part of the confusion of battle, and get in the line of fire, and it could be interesting if when they get wounded you could render assistance, and save lives, but with that you would expect them to make their way out of danger, for the majority, some as we have noted will be confused, and run in all directions.
It is a balancing act, trying to simulate battle and making that within the confines of a computer game.
All the very Best, in the endeavor!!!