How risky would it have been to take the bag through security (telling them no-one was at the counter, and you would 'gate check' the bag). Then ask the GA about gate-checking??
But still, what a mess-up by the front counter agents. This also means no agent available in case someone needed to get their BP at the counter?? Totally unacceptable, especially 1 hr before a flight.
My bag would not have made it through security. I had a leatherman and some liquids(bbq sauce that i was bringing home) in it that I didn't want to have taken away from me.