If you have an MBTA photo pass, you should be allowed to photograph in South Station, just as you would in a subway station.
However, the police may feel that they have a right to keep people off of platforms unless they're boarding a train. I've noticed that South Station is one of the few major stations on the NEC where you can access the platforms at all without a ticket. I can recall being at Union Station (DC) in the early '90's and being told that there was absolutely no way anyone was allowed outside to the platforms without a ticket, period. The fact that South Station is different probably stems equally from the fact that its really an MBTA property (not Amtrak), and the layout of entrances and the bus terminal (i.e., some of the platform area is a pedestrian corridor).
Were these MBTA or Amtrak police kicking you out? Amtrak police may not be aware of MBTA photo pass policy, however, I can't recall if I've seen them at South Station since the MBCR takeover.
Wondering if I'll see the Western Route double-tracking finished before I retire...
Photo: Melbourne W7 No. 1019 on Route 78, Bridge & Church Streets, Richmond, Victoria. 10/21/2010