Remember, the line won't be completed by December, but it will be useable. Any meets between SF and Sterling will need to be moved one way or the other. This will also probably hurt NS if they want to run an H07 type train while blocking a main track to work Hillburn.
As far as the NYSW, I believe that NS and CSX probably threw them a few bones to keep them quiet during that time. There was a lot of talk going on around the time of the merger about the NYSW joining forces with a Canadian Railroad to gain access to NJ. The day they signed the buyout is the last time they were relevant in main line railroading in the northeast, but it did keep them afloat. CSX is also probably happy to have an emergency route if they dump a train or gridlock themselves in NY State.
I think it may be possible that NJ Transit might not be the perfect, infallible organization that most people assume it is.