What if they missed a wheels up time and then timed out while trying to get the non-revs on? I agree it sucks but if faced with that choice and a hostile gate agent, what is the crew to do? The Captain can control the jumpseat but not the seats in the back. On a clear blue day with all the time in the world then yes I would agree. It sounds like there were a lot of factors in play in this situation.
I was faced with a similar situation once but with a very nice gate agent. She got the non-revs on then seated them in the computer after we pushed (at least that is what she was going to do).