If they throw out the individual mandate, but leave the rest in place, it is the equivalent of the Supreme Court having a Line Item Veto, which they ruled as unconstitutional for the President!
That's the severability issue, and you're right about the implications. It was also noted by the Court that Congress had a severability clause in Obamacare and then specifically threw it out. So it's not likely that it will be acknowledged as acting. Which means when the individual mandate goes, all of Obamacaer goes with it (which would be true financially even with severability, but the Court will just strike the whole thing outright).