Here's a quick fix for your problem... no .sqm hacking, config.cpp editing, or addons required ;D
Thanks to the Tomb Monster for pointin this one out to us :thumbsup:
All you have to do is group your civilians to an East/West/Resistance unit , and then kill that unit right after the mission starts using a setdammage command....
The leader (West/east/res guy) gets killed.. second in command (Civ) takes over and follows all remaining waypoints thinking that he is on the same side as that initial officer...
Try it out.. group one civ to a west guy, and one to an east guy, kill off the soldiers, and watch your civs get in a nice shootout