I think JB has to go. The only think that makes me say it does not have to be immediately is that there's no indictment at this point, and we don't know 100% of the facts. I'd expect that situation to be nearly resolved by the beginning of next season.
JB is the face of Syracuse University. Calling the accused liars was one of the worst PR moves one could make, and reflects directly on the University, not just JB. This is equivalent, from a personal/institutional damage sense, to a political candidate making insensitive remarks like the VA governor referencing blacks as "apes", or Gilbert Gottfried joking about the Japan tsunami. When you are in a position of power, or representing an entity, you can't go off the cuff like that. If they keep him, SU will for a long time be known, rightly or wrongly, as the school that cared more about its program than the fate of kids.
This decision should come even before the issue of what he should have known, when he should have known, etc...