My opinion, have them replaced. The dealer should take care of the replacement and paint cost. Personally, I would not risk a faulty repair job with regard to the side sills (although I do not know how significant the damage is). Additionally, (according to my tech) the newer side sills come equipped with better heat shields than the earlier years (thereby reducing the risk of yellowing). Go for the replacement, you'll be happier with the end result.
-Will