If you bring a Scarab or Armadillo APC to a haven defense, give that APC a free action ability that changes civilian/non-combatant behavior in an area around itself, telling them to get inside the APC for protection. Once they board, you can use another ability that has all the civilians disembark.
I understand this might break the game a bit 'cause you could then just drive the APC around and avoid enemies, though. If so, perhaps instead just make an ability that influences the civilians to keep the APC between them and nearby enemies, either using it as cover, or as a distraction for the aliens. Something similar could be made for your soldiers, as well.
Or, instead of an ability that affects civilians, this could be part of their AI. Have them check if armed friendlies or armored vehicles are close enough for them to reach the safety of, and move towards those for protection.