There is a customer service person at Specialized that are trained to deal with issues like this between customers and bike shops. First, I would suggest that you try to work it out with the bike shop. Tell them that you are not satisfied and you are very aware of the touch-up paint and work to cover-up their damage. Second, contact Specialized customer support and inform them of your problems and that you are trying to work it out with the shop. If the shop is unwilling to offer you a full replacement, then put in writing this to Specialized.
Your fork has been damaged by the shop and its value significantly lessened by the shop's error. For all you know, the fork may have cracked and not just scratched since you cannot see below the epoxy and touch-up paint the bike shop put on your fork. I don't know of many people who would by a cracked carbon fork like that off of Ebay. It may still be usable now, but carbon forks are no place to screw things up. Who's to say that the damage on carbon fork doesn't develop into something more severe a year or two down the road.
The shop is fully at fault here. If you still want to use the fork and accept a refund on service for the shop's error, that is totally your call. However, you are fully within your rights to have a replacement fork provided to you by your local bike shop (Greggs Greenlake of Seattle).