I use spears and billhooks (billhooks are safe, spears are more accurate). If you have some people with Fortified Mind perk you can send them out ALONE to kill enemies. Why alone? Because the perk doesn’t protect from morale checks that happen when your battle brothers see allies fleeing in terror. Other than that I cannot say, because I don’t think there is another way of dealing with them (although some people said that highly leveled up archers can kill Lost Souls from afar).