As far as the white looking scratches on the G10, I would wash the entire knife with dish soap and warm (hot) water and a toothbrush. Then I would blow it off with some compressed air and dry it off. After that you could put a bit of WD-40 or mineral oil on the G10 handles and rub it in a little bit and then dry it off with a towel. That makes most G10 look and feel like new in my experience.
As far as the blade being off center, unless it's rubbing the sides I wouldn't worry about it. I have had a few that have been off center and they still work marvelously.
If you're worried about it at all just send it in to Spyderco for a look over and a sharpening and it will come back like new. Trust me, they are really freaking good to their customers.
All is not lost. You have to awesome knives that with some Spydie care will be like new.
I'm pretty sure they will sharpen the Civilian as long for whatever the normal fee is (I thought it was $5.00 but I'm not sure). Of course it will probably be more if the thing has a busted tip or has been crazy abused or something.
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"Knowledge without milage equals bull***t." -- Henry Rollins