Nate, so the lighting board is still detecting polarity changes and the headlight in the forward direction is lit but not the other headelight, is this correct? If so, this is what you want. It is not typical that a head end engine will run with front and rear headlights on. Maybe this is a P&W thing bit most railroads dont want to burn out headlight bulbs lighting up nothing but the front most car of a train. I suspect the engineer just forgot to turn off the rear headlight. The only time I've seen rear headlights in common use is during bad weather at night when the Rule 17 dim headlights would be left on so it was easier to see if the brakeman or conductor had to move between engines. The only time this would change would be if an engine is acting as a rear end pusher. The bright headlight is usually on then. Even this would only be a problem if the cab was facing the rear, since the rear headlight would be on but not the cab headlight.
This would be easy if you had DCC. Since you don't, and if you really want both head lights on, you'd have to take the lighting board out and wire the headlights to the trucks. You'd put a magnetic reed switch in-line with the two sets of wires. You could then turn on and off one or both headlights using a magnet from the outside of the shell. You can get all these parts at Radio Shack and, since you have an empty shell, you should have enough room to make it work.
I guess my question is how important is this to you? You'd be going through a lot of work and money so you could do something that's not common on the vast majority of railroads.