I'm looking for advice on how to deal with this situation in the future- I was denied entry into the terminal area by a TSA agent because my company does not leave from the terminal of the airline that I was trying to jump-seat on; she insisted that I go to the check-in counter and get a boarding pass for the flight. Being the busy travel time that it is, by the time I was able to get assistance from the customer service agent, I missed my flight. That's after being at the security check-point an hour before departure.

Does TSA have the right to do this?

I didn't realize that they could as I was in uniform and displaying a valid ID from a US air carrier.