That seems like an obvious rule to change:
If a passenger is checked-in without the SSSS, he or she should not be subject to a change of status prior to boarding. Unless the passenger changes his or her mind and--at the gate--decides to pay cash for a ticket to Beirut with no checked bags, it makes no sense.
One of my coworkers just got sent back to the checkpoint with her whole family. I think that actually CREATED a security threatl; she was ready to kill someone at that point.
"Hi, your flight's been cancelled. And now we think you present a risk to the nation's security because of that cancellation."