I find this conversation interesting in that CSX is not new to operating over passenger networks and should be a strong contributor to a more efficient joint operation. In fact, they operate over several to include the Northeast Corridor, MN, Metra, VRE (see the latest deal), NJT, MARC and MBTA South Side. Certainly no need to reinvent the wheel here, I think CSX will have a better handle on the joint territory than Pan Am ever did.
In retrospect, some believe Pan Am was an ideal partner to MBTA by letting them do whatever, but in reality Pan Am was a terrible partner. They reaped benefits of better infrastructure without much contribution. They ran trains with ailing locos that would break down, gum up the works for a several minutes to hours. They didn't work collaboratively with MBTA to plan more efficient capacity and inter-line connectivity. For instance, I've heard crews tell me about locations of switches in the T territory that made some switching work take much longer than it should, or were simply non-sensical to the freight operations.
And let's face it... MBTA is no champion of efficiency either. How long have they been working on certain projects? Someone like CSX would be a valuable stakeholder with resources to push along projects such as the Merrimack River bridge (will it ever be done?) and relieve other bottlenecks. MassDOT doesn't seem to have much going for them in the strategy, planning or relations departments I can say that much.