We don't have the precise nature of the problem with this aircraft, the captain's views on the matter nor the AOC holder's. There's been lots of mention of the "Minimum Equipment List." Are we getting confused about the DDG here? Another document to consider is the Company Operations Manual. Was this a technical problem or an operations problem?
While the DDG is covered by commander's discretion, the flight operations management can, and frequently does, disagree with an individual Captain. In the event that such disagreement cannot be resolved, management can at its discretion, assign another captain to operate a flight. While an aircraft captain does have discretion, the AOC holder's discretion can override it. All we can tell from the story given here, is that is exactly what happened. Any discussion of the rights and wrongs of the matter must, as in the case of the Groningen incident, await the facts.