I saw our previous '04 with its roof racks off when the supports were replaced after they became badly oxidized (they're aluminum IIRC). It's a fairly easy job to remove the racks themselves - a thumbnail at the leading edge of the front should be enough to pry the front ones loose and (again, IIRC) that exposes two good-sized torx bolts. Loosening these will allow the front supports to be removed. At this point, I believe that the rail can be removed and then you can work on the rear support.
As for what is underneath, I do not recall how finished it is or if the female hardware is on or below the surface - either way, I would imagine that the patching and painting wouldn't be easy. OTOH, if the support hardware is below the surface and all you have are holes, you could very well fill the holes with body-colour plugs such as these:
http://www.bumperplugs.com/BPindex.html. If this is possible (and aesthetically acceptable to you), you might get away with an entire roof re-paint - you would just have to be sure that the holes were extremely well sealed...
