Captains have very little say in boarding-related matters. Airlines have systematically eroded captain authority to the point that captains have actually been reported to police for interfering with gate agent duties.
Everyone wants to see this captain hung out to dry because he didn't act to intervene. Pilots are perceived as sky gods by many, neutered by company policies in reality, and thrown under the bus when the company or traveling public need an 'out'.
You can't have it all ways. It's part of the reason this job isn't worth that much anymore.