Good luck in sorting out a protocol for that one.
Trouble is, you cannot easily have a protocol for over-riding the chain of command.
As in the JetBlue case, and other instances of an FO "intervening" in what, retrospectively, turns out to be a good decision, all seems good. In flying terms verbal intervention is advised first - but ultimately (for Flight Safety) it is vague when the FO can say "I have control" (even though required).
Extending that protocol to require a CC member to override the Capt's command, when in either case (i.e. the CC obeys or overrides) the result may be a hull and all pax loss - or far worse
It is easy to think of / cater for the typical personalities and situations - but we need to address the exceptional.