I remember seeing this question posted on the old version of these forums. It's a great idea, and recently CSX has done exactly that during trackwork on the River Line, but using the Hudson Secondary as a bypass on a regular basis probably wouldn't work out all that well, for several reasons.
First, the Secondary between Hudson Jct. and Warwick, NY is owned by NS. South of Pelton Road in Warwick the trackage is owned by the NYS&W. On the north end the Secondary ends at Hudson Jct. where it meets the NS/NJT/MN Southern Tier line. Assuming that ownership doesn't change, you would need to have trackage rights agreements set up with NYS&W, NS, and NJT in order to move a train in or out of the NYC metro area. Speaking from hands-on experience I can tell you that any train that wanted to go from Hudson Jct. onto the Southern Tier or from Port Jervis to Hudson Jct. would have to wait until we had a window between the commuter trains. With the increase in trains that NJT is now running out of Port Jervis that window has only shrunk down. It would also be the same for any train waiting to get onto the NYS&W. Increased business from Little Ferry all the way north to Sparta would also probably delay a train more than help it along.
Second, the trackage probably needs to be upgraded somewhat to handle heavier trains than the line currently sees. Yes, NYS&W did do extensive upgrading back in the 80's when it first started running stacks and haulage trains between Binghamton and Little Ferry, and they have kept the line fairly maintained, but I don't know if the line could handle heavy freight trains on a somewhat regular basis. Susquehanna's SU99/100's and locals that currently run on the line are generally short, lightweight trains compared to what NS or CSX would run if the route were used as a bypass.
Anyway, just a railfan's thoughts.
Joe P
Long Live The EL
www.geocities.com/jmpwpd29