I wonder if Greenbush-Braintree shuttle trains in regular service, via the wye, could be theoretically possible to fill in some of the gaps (perhaps same with the other Old Colony lines to Braintree). The Old Colony single tracking must make scheduling a nightmare; this could be a good way to provide more service. The idea of having to change trains for some runs will definitely ruffle some feathers, but it's better than a giant gap in service.
Of course, this idea would be a lot more feasible if the Red Line ran at anywhere near normal speed and frequency, making transfers much less dependent on the timeliness of two infrequent commuter rail trains.