Are you also using the "setFriend" command? Maybe you have setFriend civilians to be friendly with the West. And since you edited the civilians to be on the East side, they start shooting the other civilians because their base class is civilian, and friendly to the West.
I only say this because when I first experimented with setFriend and set civilians friendly with the East, the RACs started shooting at empty civilian vehicles...
By the way, I am still without an Arma capable computer, so haven't been able to try your new mission yet...