To say the Captain left of his own accord is like saying Rudd stepped down because he thought Julia could do a better job than he could.
The Captain basically failed in his duty to monitor the other pilot who was PF. The report also states that the Captain's response to the aircraft not being stable was to put the gear down and apply forward pressure on the side stick! The F/Os reason for disconnecting the A/P was flawed and both pilots could have taken the opportunity for controlled rest on the way from DN if they were feeling tired. Blaming it on fatigue is a bit rich as they both agreed to fly it back to DN on what was the worst part of the duty, the BOC part.
The incident occurred because of a complete breakdown in crew co-ordination. Who is responsible for that? Ultimately its the bloke who is wearing the four bars. Some people like the paycheck without the responsibility. As it has been stated many times those who think CRM is a load of PC crap are the ones who need it most.
Certainly not one of Jetstar's finest hours but they have to work with what they inherited.