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For all we know. We don't even know if he can be killed; that blue skin has always made me picture him as some sort of energy being. For narrative purposes, I think he will still be alive. Mainly because he'll be making his reappearance after Jack has regained hope. Of we were still hanging out with Punished Jack the death of the Guardian and the destruction of the portal would have been a major blow for Jack. Now, with Jack back to full strength I can see his reappearance being played as one final chance to return to the past once Aku has been dealt with. Genndy probably wants to address the dilemma of whether going back to the past is the most ethical thing to do or not, specially for a man like Jack whose moral decisions have been for the most part very cut and dried.
