My suggestion is to group empty vehicles and all objects that have no crew in them to the Logic side instead of Civilian side since it creates enormous problems when you make civilian side your enemy: AI starts to engage empty vehicles (not sure if this is still a case in A3, but definitely was before), you can't open inventories anywhere, and so on. Since there is no way to create new sides through script, there is just 3 normal sides in the game while Civilian side remains crippled like this. I believe its time to change this ancient order of things in ArmA 3 and make civilians fully usable side that functions exactly like other sides.
This will also will require setCaptive to move player into sideFriendly or sideLogic instead of civilian as it is now. Currently AIs never engage sideFriendly or sideLogic units so it will make setCaptive work as it worked in all games before.