Here's a list of the few people you don't need to kill

The Allies
Name Description Picture
Scientists These are very useful for opening security doors and giving you information.
Security Guards (AKA: Barneys) Security Guards are the only people on your side that have weapons - they can help you through some nasty fixes. They can also open security doors for you, although I thought that would be obvious.
The G-Man (AKA: The Man in the Blue Suit) Not much is known about this guy, but you see him quite a lot in the game. He doesn't hurt you, so I suppose he's an ally.