Hello, it is a quite long time I stopped editing but as far as I remember there are two ways to do what you ask:
1) Group any civilians unit to a leader who belongs to enemy side (if you are NATO, you group all civilians to an East unit with upper rank; if you are East, you group all civilians to a NATO unit with upper rank; if you are Resistance, you either group all civilians to a NATO or an East unit and make sure Resistance is "friendly to nobody"); then you edit NATO or East unit you placed in the editor and set "Probability of presence" to 0 (cursor all moved to left) to "delete" that unit when mission starts.
2) You either add this addRating -5000 in every civilian's init line if they are lone units or you group all civilians to one civilian leader with that init line and an upper rank.