So, I actually think Sam just standing there when the gun is leveled at him is the writers not forgetting about the Mark. Sam is stunned at the cool casual way Dean has just murdered this guy, a slow steady stab into his gut while the guy is still holding the knife. Sam is shocked at this, and it allows Ghostfacer guy to have to jump in front of him to save him from getting shot. I'm still of the opinion that Mark of Cain Dean and Dean the Cold-Blooded Hunter aren't necessarily different enough to be visible without some really serious work on the writers' parts, but I tied those two events together on my first (and only) watch. I still need to rewatch, but this was my initial impression.