That does not sound accurate. The 'ghost' station described is an original, pre-extension station. When the line was extended beyond Harvard Sq., they moved the station just up the street around a sharp bend.[1] Very MBTA. I respect the journalistic source, but it seems exceedingly unlikely anyone ever tried to cut off the existing station and run it through Harvard Yard, much less got so far as to construct a ghost station.

[1] https://en.m.wikipedia.org/wiki/Harvard_station