I don't work for Mesaba, so I won't try to guess an answer to your company procedures.
However, last time I checked, the jumpseat belongs to the Captain operating the flight. Someone at the gate insisting that its their jumpseat over someone else doesn't seem quite right. I am an old school believer that even if you have a seat in the back and are technically a jumpseater, you need to come to the flight deck and ASK permission for a ride. That's protocol and I think that very few people will disagree (by the way - if you are a Dispatcher, this also applies to you!).
I know the jumpseat order at my company (and I have a reference card that I carry as well). But if two pilots from my company had a spat at the gate similar to what you are stating, I would take the one that was NOT yelling at the gate agent or a fellow pilot (regardless of seniority).
The way that I look at it, the gate agent shouldn't be making the final determination. Either the gate agent should ask for the Captain to come to the gate or both of you should go down and talk to the Captain. End result - Captain has final authority as to who gets the jumpseat. Also, if I get input from the gate agent that you were creating a scene at the podium - plan on not getting a ride (as long as I feel that the gate agent isn't lying).
It sounds like you handled it appropriately. If you have a jumpseat committee at your company, I would suggest calling them and have them discuss this issue with the "attitude" pilot.