At AE (and therefore AA, I imagine), we do not have the authority to force a gate agent to board anybody. The company has made it very clear that not only will the gate agent win the battle, but we will be held accountable by the chief pilot's office if we attempt that battle and cause a flight to be late. Written up. Letter put into your file, etc.
In this case, it seems that maybe there was a wheels up time to be made. It would be wrong to miss the wheels up time because one was diddling around trying to get non-revs aboard. It sucks to be them, but it would REALLY suck to be a paying pax and be delayed even further because we missed our wheels up time because the captain was trying to get more non-revs onboard.
I've commuted off and on for 22 years - and I do it now. Commuting can be perilous sometimes. It is what it is.