I would bet $100 that Jack's dad is not dead. Think about it, he was wounded about 3 feet from a perfectly functional boat. Jack ran upstairs and Naudia said to Bill, "you've got 90 seconds." That was after Jack started up the stairs so we're talking about Jack's dad having about 2 minutes to flip over into the boat and ride away. The Chinese sub was pretty damn close by and Jack's dad could have conceivably boarded the submarine and received medical attention. I firmly believe that season 7 will include that exact scenario, and Jack's dad will be pulling triggers from China. And there will be some kind of Chang for Bauer type climax.