I think Alex can't bring himself to pull the trigger, because he's seen it too many times and knows too well it's irreversible. He probably can't let himself get carrid away and shoot in cold blood. That's probably why Anthony Horowitz wrote his that way, so we would have more respect for him.
Yeah. And to add to that...if Alex joined Scorpia before knowing about M16, he'd probably be able to kill. Possibly. Well, since his uncle, and parents died, maybe that's why too.