In my experience, resurfacing doesn't hurt the value, it helps it. You take a $20 game with some light scratches, now it's $17 or so. Resurface, back up to $20.
As for the ultra-rare games, there it becomes a matter of taste. But if I was planning on selling Popful Mail complete, with a working but hammered disc, I'd get it resurfaced. And get more money for it.
So, if you wanna keep it, ask yourself if you care or not. If you intend to resell, nothing looks better on a disc game than 'No scratches'.