Icarus,
I never suggested the Captain confronted the passenger but he should have been informed of the situation in the cabin and not left the flight deck even if that meant pissing in a bottle or on the floor or diverting the aircraft to the nearest suitable airport if he had to go.
Lets say he even had a gut full of nasty from the cheap vindaloo the night before and did go to the loo, there are other things which could be done so that the convicted passenger could not approach him. Blocking the aisle with a cart or using ABP's to prevent the passenger entering the galley.
This incident should and hopefully is being internally investigated, these pilots do their Security Training with the Mainline pilots and should not have allowed the situation to occur as reported. If the Captain went into the cabin with the knowledge that a threat has been made on his life and the safety of the aircraft then I believe he would have been in breach of company procedures and would ask if retraining or disciplinary action should be considered.
The days of going back and working things out left the station years ago. If the FA's down the back are too small or weak to cope then they should use ABP's or what ever they can but the flight crew should never compromise the safety of the aircraft. (LARGE CAPITAL FULL STOP)