I ride the MARC almost every day that I'm in town. At the major terminals (like Union Station and BWI), their counter ticketing is done by AMTRAK, hence the ID harassment. At the expense of using your credit card, you can buy a MARC ticket from the AMTRAK ticket machines. Also, you can buy a MARC ticket from anywhere to anywhere from any MARC manned station (such as Silver Spring, Germantown, or Brunswick) by cash or credit card without the ID intrusion. Look on the MARC website and you might find that there's a manned station fairly convenient to you.

Every member of the MARC crews I've ever met have been great people (if not a little crazy). I've no doubt they would tell the TSA to stuff it by just ignoring their direction.