Jack killed him off last season -- and if he's ever put on trial for it, no jury would convict him. He was working for "the man," and nearly exposed Sydney as a double agent. Jack doesn't like people who betray the CIA and put his daughter in danger.
I understand that Ariana Kane will find the gun Jack used to kill Hadalki -- as if! As if Jack would be so stupid as to leave that lying around! Anybody who ever watched a cop show would know better than that! I wonder how they plan to work around that. Or maybe I just misunderstood.