Living in Allston-Brighton, it is really difficult to be upset about adding a yard here. As Stlin mentioned, the loss of developable land can be almost completely mitigated by building footings up front, and Harvard can basically be forced into funding them (it's not like a few hundred million would ruin their ROI here). Walking to the station from south of the Pike might be a minute longer, but that's small potatoes. And assuming there will be diesel equipment here for the foreseeable future, having shore supply at all the berths will prevent any of the problems associated with idling.
Any issues with the rail yard are minimal in comparison to the existing 8 lane highway that will continue running through Allston. Poor use of urban land, noise and particulate pollution, and a lack of neighborhood connectivity are going to be problems as long as the Pike is there and not decked over.
I think this is pretty much where I'm at with the yard. I've been pretty solidly convinced that it's not operationally necessary, or if there's some reason to believe it will be in the future it's up to the state and Amtrak to lay that out, but I also just...don't really think it's a big deal in the scheme of things. Time and energy used on this is better served elsewhere.