You keep talking about factions, but we don't have any. Civilians are humans, if that's what you mean. They're AI controlled, so they're on a different team, but they're not a "faction".
You can't edit their equipment, because they don't have any. All civilians start unarmed (though infected ones will start with alien weaponry - but this isn't finished yet).
Their behavior is dictated by the AI. If you change the AI so civilians will never shoot at you, you're set.