I found a great deal on a KHS 2003 model Flite 100. But there is a small dent on the top tube about where a top tube protector would go. It's on the side of the frame running perpendicular to the top tube. Apparently it happened during shipping (he bought it off ebay and is now reselling because he doesn't ride it). The dent isn't too big nor is it too deep. Cosmetically, it isn't noticeable, but you CAN feel it. Is it worth it? Would this ruin the structure of the frame?
Frankly, since the Flite 100 is a steel frame, you'll be fine. My Surly Pacer and I were involved in a high-speed downhill crash this summer, and it got the same "handlebars-into-the-toptube" dent that it sounds like you've got. Not nearly as drastic as dude's C-dale above, and because steel doesn't crack/fracture as readily as aluminum does you're good to go.
You've just got an inadvertant "Cat 5 pimple".... love that term ;-)
Small dings in the TT & ST aren't so bad. It's the downtube that you really gotta watch, that's the serious structural component of the front triangle. That's why bikes with oversized tubes start with large dia downtubes.