Well, yeah - but Jack sort of deserved it and he didn't die nor did Owen intend to kill Jack and well, Owen knew at the time that Jack could survive it.

In this scenario - John killed Jack. (Granted Jack is unkillable, but he did not know that.)
Tried to kill Gwen - by poisoning her, pretty nasty way to die too - if the others hadn't come in time. He shot Owen and locked them in the room. Granted that wasn't fatal. Oh, and, John had no qualms about letting the world blow up.

You'd have to be an idiot to let that guy on your team. Not that I think those were Jack's main reasons. (John knows far too much about his past - Jack wouldn't let him on the team for that alone.)

Yeah, he'll be back - I think in the next to last episode of the season. They apparently love him over there. And he's gotten rave reviews on both sides of the pond for the role.