There are only certain people allowed to ride for free. It is the train crew's responsibility to collect the proper fare. These days there are spotters all over watching, just waiting to pounce on an employee not doing their job properly, including collecting fares properly. The real professional courtesy should come from the MTA employee looking for a free ride. It should be understood that if a free ride can not be given, the argument should be dropped. The person asking for the free ride should do so in a discrete manor as to not draw attention. The employees from the other branches should remember that when they are on duty, they have a job that they are expected to do by those who sign their checks. If a courtesy ride can not be given, the person asking for the courtesy ride should have the courtesy to not harrass the on duty employee for doing his job, and just say "well, maybe next time". That's the real courtesy. You also can not expect to show up to a train with five friends, arrogantly flash your MTA ID and expect a free ride for all, in plain sight for everyone to witness.
Sorry for the somewhat rant, but courtesy goes both ways.