2 Dogs, I'm going to put in my 2¢ at this point.
From what you've said about the 2-year warranty being good till 11-2012, I'm going to go out on a limb and guess you purchased in November of 2010.
You said you brought this up to them months ago. Based on that I would say that you didn't notice this for more than a few months before asking the dealer for help in getting a new fender. I'm not saying that it's not going to be covered by the MOCO, but most manufacturers try to take care of paint issue as soon as possible to the delivery date. Anything longer can just complicate the issues as possible environment issues versus factory issues. Again, I'm not trying to say this was not there from the get go, it's just harder to deal with after some time has gone by.
I'm wondering why you didn't notice this the first time you did your cleaning detail on the bike?
I had some "smoke" in the paint on my tank when I bought a new '08 SERK Annie. I tried my Dupont #7 polish with a mild buff and it didn't come off so I brought it to the dealer's attention by phone right away and then a couple weeks later in person. They had the bike for the 1,000 service and when I got it back the smoke was taken care of. They got a little more aggressive on the rubbing compound than I did and it work out great for me. I doubt from your description that this is a surface clearcoat issue so rubbing and or wet sanding will not work, replacement is the only fix.
As far as going over the dealership's head, if handled correctly they may be in favor of you doing that. In my case with my newer '09 SERG seat gap issue, the dealer had done everything by the book and it was still not fixed. I asked them what I should do if they are at their limit of action, he told me to call the MOCO and get a case file number and see what they will do for me.
Maybe the MOCO rep told the dealer no on your paint, so that's really all they can do. Now they could be your advocate and aggressively persue the MOCO on your behalf, but that doesn't happen very often. I would not feel like you are going behind their back at all. I would, like others have suggested, go to the GM of the dealership or owner and let them know that their service department has apparently tried to get this resolved, but cannot go any further. You feel now that it's time for you to report the obvious paint defect to the MOCO and start a customer case with them. He should not feel threatened that you're going to complain about them, but that you're trying to let the MOCO know that you are going to persue this further. My seat issue ended up as a tier 2 level and I got some action when I reopened the case.
Good luck with your paint issues and let us know how it turns out.