They'd better have some kind of deep cover story for Tony. It wouldn't make what he did to Larry okay, but at least it's a million times more interesting than bringing a beloved character back from the dead just to kill his character in a completely different respect later in the season.
There is no deep cover story for Tony. Remember he was a mercenary after his wife died and committed acts of treason that made him a wanted man.
I would bet if he didn't hear about a cannister of the nerve agent was in play he would have gone into the FBI with Larry and spilled the beans on the new bad guy.