Obviously, you want to avoid disturbing the factory finish, but if this blemish is noticable I wouldn't hesitate to have your dealer refinish the panel. I assume this dealer has state of the art facilities and highly qualified people. With the right equipment, products, and techniques, paint repairs can be virtually undetectable. On the other hand, in the hands of the wrong people, it can have disasterous results. Do not, however, insist that they replace the composite body panel because of paint problems. It would be a major job, very intrusive and unecessary.
Painting is routine, replacing composite body panels in not.
Painting is routine, replacing composite body panels in not.