I'm not seeing how the issue in question is a "perk" for GM or higher and that the agent should be chastised or worse for allowing the passenger on the aircraft. Other than security issues (i.e. checked bag on another flight), how is it possibly beneficial to the airline that an aircraft would leave with empty seats (assuming no overweight/out-of-balance issues) while a standby passenger is waiting at the gate with a confirmed ticket on a later flight? I would think it wouldn't even have to be a skymiles member, just a customer with a ticket, to get on the plane.
This reminds me of the scene from that movie where the gate agent is only boarding rows 30-35 or whatever, when the only person in the entire gate area is sitting in row 12. "Sorry sir, you have to wait for your row to be called." And then they both stand there in silence for 2 or 3 minutes. "Now boarding rows 25-30." etc.
Maybe it is "policy". One that needs to be changed.
SR