But for the security restriction imposed by the RNC, which make all trains reserved trains, you would have been able to use your ticket in reverse.

As long as you are not changing the city pair, which you indicated is the case, the conductor wouldn't care that your ticket read WAS-EWR and you were trying to travel EWR-WAS. The value of the normal ticket is the same and therefore Amtrak wouldn't care.

If you ever did get a conductor that gave you a hard time, just tell him that the northbound conductor lifted the wrong ticket.