Nice time lapse concept, but maybe you can try shooting from a different vantage point to avoid the headlights glaring directly into the camera.
If you move further across the footbridgeto the west, you run less of a risk of getting headlights directly in the lens.
here is a link to one of mine as an example. (won't post the pic here, not trying to hijack.)
DSC_4948 color | Flickr - Photo Sharing!
I realize that doesn't give you the same composition, but it does offer a potential solution to the issue. The good news is that vandalism is in our favor there, and there have been holes cut in the chain link fence at several points all the way across the bridge.

Another thing to try is to get the same shot in the morning just before sunrise. The light is really quite different, and not as many people have their headlights on.
The problem is, there is an element of crime in that area. Not terrible, but if you go hundreds or thousands of dollars worth of photo equipment, I would at the very least go with a buddy or in lieu of that go armed.
Again, this is my opinon. I realize that the opinion of others may vary wildly.