Can't really see what's going on in the photo directly above, but the other photos showing rust around the nut serts look to be fixable. I would first sand that area by hand to see how it cleans up, get it down to bare metal but there will be some small rust pits, that's when you carefully apply the Phosphoric acid type rust killers, just follow the directions. Once that rust is stopped you can prime then paint the area. For a quickie paint job just get some painters tape and tape off an area around the nut serts then paint, no one is going to see your roof as you roll down the road.
If you wanted the paint job to last a bit longer than just cheapo rattle can paint you could use a 2K (two component) aerosol paint in a spray can (SprayMax primer and paint); it's not cheap but it will last much longer than the other stuff)
Or, next down in cost is SEM primer and paint; it's not 2k, but better than your average rattle can paint.
If the body color is ?White Duplicolor has a White color EBTY15787 that is a very close match to the original 045 White, no one will notice the slight difference on the roof.
If you want to keep those threaded holes you could use a new stainless steel screw with a thread sealer on the threads before you install the screws. That way if you or the next owner in the future wants to reinstall the roof rack or anything else, they can remove those screws.
Otherwise after you've killed any rust on the threads you could fill them with a two part epoxy (Permatex or JB Weld) then sand, prime, and paint over it.
Yeah I'll stay far away from bad silicone. 
