I agree with Maxwell, especially if they said you can get the door replaced at anytime in the future. (just get it in writing). If you cars windows seal well, and the door closes the way it should, why take a chance of them screwing it up. Besides, they probably couldn't match your paint either.
The temp fix (if it's done like Andrew did his) should fix the problem permanently.
What really astonishes me, is they said it's covered under warranty. Usually "surface rust" isn't.
Your case should be documented for future reference on this forum. So when others try to get their dealers to do the same for them, all they have to do is bring up your paper work just in case their dealers are unwilling to do anything about it.
Thanks to you, a precedent has now been established.