you have to change the side of the units in the 'mission.sqm' according to what you want, like:
you have the NATO guys as "WEST", soviets as "EAST"
and if you wanna make them kill civilians, then i suggest to set the civilians side to "GUER", then you can set whether the soviets "don't like them" or the NATO, [in the mission editor, where you set the weather and stuff..]
i dunno if it's understandable, but just write me on msn and i'll explain better ;D
There is easier way to do it. You need to create west or resistance unit, no matter what. Just make it leader to civilian and set probability of presence to 0 and there you go, they shoot you down !