You could cover up the scratches with a cover cheaply, but it would get roached if you go down again. You could replace with the billet covers. Heavy duty and protect well, little pricey. Are you looking for protection, or looks. Personally, as long as it wasn't damaged, only cosmetic, I would get the covers. If it was damaged and had to be replaced, I would get the HD billet covers.
Hey, I don't know if this will work, but I thought I would let you know about it. I was at Lowe's this weekend and in the paint department by all the caulk and tape there was this liquid shit that turns to rubber...like on your wrenches. Well, it came in black, red, and yellow. I didn't read much about it, but it's worth a try. I might try it on my old oil pump cover as a test.
the only "mod" I've seen to stock case covers to make them more durable was on a CBR929 out at Grattan. He had 1/8" plate welded to the sidecover... THAT would protect it...but it doesn't look to pretty.