I could be very wrong, but my MCC course went to great lengths to hammer into me that there is no such thing as 'captain' and 'first officer'. It is pilot flying and pilot not flying.
If you read an airlines SOPs or ops manuals, you will find that roles are defined as PF or PNF / PM the vast majority of the time.
Of course the captain is in charge of the ship, and there are certain responsibilites which belong to a captian only. But, if the skipper has to say 'I'm in charge and I'm over ruling you' then there has been a massive break down of CRM. In short, both FO and Captain have failed in their duties.
Just my tuppence!
EK