The switches shouldn't interfere as they don't pass through the platform or anything, and usually when the stops on the northbound side there is still about 6-10 ft of platform by the northern end staircase. If this were somehow an issue though, there are still diamond crossings south of the station.
As for 49th, there still is the during busy hours. The will still stop there on weekends and late nights, just not during rush hrs and middays. Evenings could be adjusted based on ridership.
For the issue, I would give the priority, and the could hold on the southbound track. Considering that the goes rather fast down Broadway, it would be more efficient to hold the and let the pass than vice versa.