This location is just west of the famously photographed signals at Afton. It is also east of the split for the Penn Division. Remember the main line was originally the line down to Carbondale. I would think this was the wye for the Penn Division helpers or for turning power coming to / from Binghamton and going from or to Carbondale. Due to the elevation difference between the two lines at Ninevah it may have been difficult to shoehorn a wye into that area.
There is another abandoned wye just north of Starucca Viaduct on the Penn Division, I remember walking it during the tunnel detours in 1985.
Chris