I agree. By OP's own admission, he/she did not arrive at the airport at a reasonable time before the flight, and the reason was something within OP's control.

Agent discretion is important. In this case, my opinion remains that the agent used appropriate discretion to NOT allow a rule exception.

I get that BE fares are part of the overall increase in "regular" fares as part of the airlines' revenue plans and reaction to an evolving market. I was referring to the purpose of BE fares for the airline, not for the customer.

And I don't hate BE passengers or fares at all. They serve a specific purpose and I have purchased them before. I would be perfectly willing to accept my own medicine if I found myself in OP's shoes.