Two points on this:
1) Matt Yglesias and Atrios and everyone else needs to stop playing dumb. Does anyone honestly think that in the event of another terrorist attack on the scale of 9/11 Americans won't, yet again, rally around Bush? And does a more popular Bush make for a more difficult time getting a Democrat elected President? Yes.
2) Democrats are right to disrespect an argument which basically says we should vote on primary day out of fear (in part) of what might happen if there's another attack during the general election.
Still, Hillary's assumptions about an attack helping the GOP are probably right.