For Bearfoil and Rob2:
I have studied in minute detail hundreds and hundreds of DFDR readouts/data in the study of events of various types where the F/O was PF. In many of them there were instances where it was obvious that the captain should have intervened earlier yet he did not. This where the command structure is self evident. Now we had the case where 2 F/Os were flying together. It is not surprising that there was indecision when it came to such a need for intervention. There is a very strong case for mandating that the senior (and one hopes more experienced and competent) always assumes the role of PF when the captain is absent from the flight deck. Thus this CRM issue is avoided.
As for manual flying, it is worth bearing in mind that when flying in RVSM airspace there is a requirement for the a/c to have a serviceable autopilot. Should the autopilot fail ATC must be informed and the a/c leave the designated air space. The inference is clear that manual flight is not permitted. We may not like it and the downside is obvious but we are where we are!