Go ahead and Bow Up to the TSA geeks to fight for the oppressed and oppose tyranny.
Tell that TSA supervisor how foolish the policy is and that you're going through screening with only that airline ID. Refuse secondary screening because you're going to be riding in the cockpit anyways.

Just remember to loudly scream that you work for airline XXX as they drag you off, doing the best you can to make sure you make the evening news.

Or, you can avoid losing control of the situation, write down the employee numbers, involve your union and company security folks....who work with the TSA geeks daily. Who can fix the problem? You telling the security folks they are wrong, or the security folk's supervision telling them they are wrong.