Any way to fill the Ba Bay void?
Not really, but that doesn't mean there isn't other good Vietnamese. Although the only place I can really think of that is in the district is Nam Viet, there must be others.
If you hop on the orange line to Virginia Minh's it is good, although not anywhere near the same vibe. Rice Paper in the eden center has a rather hip vibe, but not near the district. But the Eden Center is a great place to visit to wander and eat Vietnamese. I think it is a real shame Ba Bay closed too. So perhaps consider a zipcar for a day sometime to the Eden Center.