I tend to lean toward the "make it right approach" - so new bike or maybe frame. My Madone was much nicer finished then Kim's, but had a few flaws (no chips). I was once told Trek keeps their senior painters working on Project 1, I don't really know. Some people clean and polish their bike like crazy (me and Silver), others rarely even clean the chain. If you are content with a discount and a little touch up paint, that might be a real option.

A friend has a big rub spot on his new Cervelo P3, the shop rubbed it out a bit, but he said he'll just put a sticker on it - 6 months later no sticker and I doubt anyone ever notices. He just rides it like crazy.

I'm very anal, but my bike has fallen over a couple times - duh! The worse damage came when I kicked the top tube with my cleat mounting it before RAIN last year - nothing looks bad, just what happen on a bike with 10,000 miles.

My guess is Trek and your LBS will take care of you doing basically which ever you want.

Let us know what happens, and were are the pics?