I'm not sure. We only stopped it for an instant before it charged ahead causing death and destruction.
It's rather simple to do, really. Have a red engineer put a dispenser on the tracks, then have someone on the blue team stand next to the dispenser, touching it, on the tracks. Uber them when the train appears, and it will actually stop. The time I saw it done before this time, the person stopping the train was a disguised spy, and there were eight or so medics from both teams ubering him, so the train was stopped for quite a while...