haha resorting to killing civilians so they aren't turned into zombies is a great tactic that really shows how scary chryssalids really are.
If you are feeling a bit more merciful next time, chryssalids only like rough action: They will not mate with stunned targets. Thus you can save the civilians by putting them to sleep.
Early game, that means anything that isn't in immediate danger gets hit by a stunrod. That's good practice any ways, because that way they won't brainlessly wander in the aliens' line of fire, or in your own way. You can even pick up the stunned civilian and more them to the safety behind your lines.
Later with ranged stun weapons and mind control, it's even easier as you can either stun them from afar or get them to walk themselves to a safe spot.
