The grand junction was 3-4 tracks wide to Main street, so fitting in full blown transit with a path shouldn't be too difficult. There are a few pinch points where MIT built over the ROW, but it's still not too bad. At the bridge itself, if they ever need to use both bays a bike path could be cantilevered off either side, again not too too difficult.
Where it's tough is north of main street, where theres not room for much more than two tracks.
Honestly though, other than the Charles River crossing, I think it's a waste of money. I think a better use of funds would be improving/installing a real eastbound cycle track on Albany St, Portland St, and Medeiros Ave; along with a westbound one on Vassar St, Galilei Way and Fulkerson St, and tying them in to a crossing on the Grand Junction bridge. Other than Galilei Way they are basically back streets already, and have better connections to the cross streets (aka where people are actually going) then a segregated path facing the backsides of MITs labs. Not to mention, just like the SWC, Minuteman and Charles River BIKE paths, it will likely be mobbed with pedestrians walking five across on the wrong side, dogs on retractable leashes stretched all the way out, unsupervised children darting out from behind trees, and everything else people bitch about on Uhub.