Mike, there was indeed freight activity in that area into the 1970s. For about twenty years after the 1958 sale of the rest of the branch to what was then the MTA, a short section of active freight track ran across the big Red Sox parking lot from what was known in B&A days as Brookline Junction to that big warehouse (formerly the Sears Building complex) that you mention. It wasn't abandoned until Sears moved out, and the track remained in place across the parking lot for a number of years after. As for the exact former track layout at the current Green Line station, I can't help you with that, except to note that the area was rebuilt when the subway portal was dug -- the rail line just continued through there at ground level. BTW, the entire Highland Branch was double track, as it remains today.