You don't need to kill them, although with the current busted seeker AI and the gjall nerfs, they probably won't have as much trouble to deal with those enemies as they used to. They won't actually detect you if you pick up their stuff after the containers have been broken by enemies or if they meet their demise in any other way than by your hand, only if you harm them or their possessions.

However, you should also consider that they are uninvited intruders in a burial/prison world which is under your jurisdiction, and are essentially grave-robbing Valheim.