Sounds like there needed to be more communication before the game. It seems like New Player, is new and you/your GM run a heavy mirror shades style game. New player really needed to be prepared for that style.
Also, it sounds like it was partially on accident, but the GM and you worked together pretty well to screw him over completely. With a security guard just happening to show up at the worst possible time, resulting in additional bad things to the New Player.
Also, there is a line between I'm not a jerk my character is, and actually being a jerk simply for bringing that character to the game. Anyone can make a character that in character intends to betray everyone and kill the team. That player is still a jerk. While that is not what happened here, are you really certain there was no other way? You have him unconscious and subdued and hidden. Call a doc contact and give him some quick plastic surgery, face problems solved. Also, talk to the New Player out of character. So he is unconscious and can't communicate, take a moment out of the game and speak to each other about how the situation arose, how you see it resolving, and provide a chance for the players to work something out. Especially as it was already another team member and you deciding what to do about him. Or just stash him somewhere and finish the run, and come back for him later. Or even turn him in to LoneStar afterwards. There are a lot of other ways to resolve the situation than what occurred.