To me, the problem with this building is not the building itself, but the way Staniford and New Chardon St. create a block shape that conspires against anything urban. My first thought would be to break this block into two pieces. William Cardinal 0'Connell Way should be pushed east through the middle of it. The question then becomes whether that would connect via a pedestrian way (with vehicle access) that goes straight to to northern edge of Bowdoin Square, or does it continue to meet Bulfinch Place. The advantage to the latter is that it would meet square (as only a Bostonian could say) with the edge of the courthouse and neatly give the plaza real street frontage.
In the really big picture, the extention of Bullfinch Place would lead to the opening up of the real looser in this whole part of town, which is that strange set of buildings (police, post office, WHDH...), which seem to have disappeared completely from the map. Just ask yourself when the last time you were on Sudbury St. Or actually, ask yourself if you even knew it existed.