I will be absolutely astounded if they actually run any regularly scheduled service during daytime on that line. I can just hear the howls of very well to do NIMBY's all along the route. The only way it will happen is if they can find the money to did it into a trench through Cambridge.
As a Cambridge resident, I'd have to agree with you on that. Ever since the MBTA bought the Grand Junction line the city council has been up in arms about the possibility of "high speed diesel trains" (their words, not mine) running through the city. I have some rather, um, interesting campaign literature about this issue that showed up at my apartment.
NIMBYs aside, the city council does have a point that the line does cut across most every busy street in that part of Cambridge. However, I would also argue that the current 5mph switching of strings of well cars that happens there snarls traffic much worse than a 30mph Downeaster or MBTA train ever would.
It's also worth noting that the Grand Juntion would NOT be a suitable BON-BOS link. I believe it would require a reverse move at each end and would probably take at least 30 minutes to complete said connection. That's about the same amount of time as it takes to walk between the two stations.