"I have heard of a flight crew many years ago being suspended for going against the wishes of the company when they were requested to delay a flight to wait for a lot of late pax but didn't and carried on and departed to schedule."
Good for the company. Unless FTL Discretion or a dire safety factor was involved, I can't see how this Captain considered himself to have the authority to make such a commercial / operational decision off his own back.
Operations Departments are far better prepared in strategies for moving aircraft and passengers around to minimise expense and overall disruption. Too often I have witnessed pigeon-chested attitudes of Captains exuding power and authority outwith their remit. They are usually the ones who refer to "my" aircraft and "my" crew. CRM is company-wide through all an airline's departments; not just confined to the aluminium tube.