These can be counted as not really enemies, but if you wish, once you obtain weapons, you may kill them.
The Prisoner in High Secruity Compound that can't be killed by bullets can be killed in a long process. First, use the all weapons cheat and free him. Second, take the normal path until you get to the bathroom area. Next, shoot him and move the block so you can fill up the room with water. Last, push the button that fills up the room with water and you should hear a groan, that means you killed him.