I suspect that the easiest way to accomplish this for command control engines would be with the sensor track as GRJ suggests. You could program it so that when passing the sensor, the engine comes to a stop, then starts up again after some amount of time.
If you want to get really complex, you could also build your own device that senses a train, and sends signals to the legacy base to stop the engine, then start it up again. It gets really, really, complex if more than one engine is going to be passing by that station, but you can do neat things with different engines stopping or not stopping as you like. the sensor track method is much simpler.
JGL
