Well, going through tunnel 6 would put the railroad depot right in "downtown" VC, with some room for switching--but not only are they worried about the construction disturbing the church, but also the vibrations of the train running through the tunnel.
Now as far as a really useful tunnel repair, Tunnel #2 would be very useful, though it will probably require a concrete liner, or even a "cut n cover" construction (cut the hill through, put a roof over the tracks and fill back in). Then that really sharp curve that's hard on the engines goes away and improves operations. It's a shame that ridge over #2 is so unstable.