Like pus said, Civilians should be a wild card.
Whoever "wins" their support they will help.
At the start they should be looking out for number one (themselves). as the game progresses they should reconsider their objectives.
If a CT kills a civ they'll want to take revenge and side with the terrorists. Likewise if the T's kill a civ they'll want to side with the CT's. The T's and CT's should be trying to win over the civ's to their side. Giving them offerings (weapons/ammo), making backroom deals and such should be encouraged.
Make some sort of "decision tree" kind of branching for the civ's objectives depending on what they do and their behaviour. At the start they should be neutral but gain "points" ie:
100 (T) < ------ > 0 (neutral) < ------ > 100 (CT)
Civs should also maybe have limited amounts of ammo at the start but the different teams can give them ammo/weapons to help them fight but not supply with too much ammo since they could turn at any moment (since they're like freelancers).
Civs should also possibly be split too. ie. one side of the town might want to help the T's fight "western aggression" or whatever, and the other side of the town might want to help the CT's stop the spread of "extremism/bio-weapons"