Rust on the surfaces of the pads & disc could cause extra wear & noise, or if bad enough reduce the effectiveness of the brakes. If there is enough present that you can see residue on your finger after rubbing the surface, I would suggest cleaning with a stiff bristled brush or a kitchen scrubber & isopropyl alcohol (some people have recommended automotive brake cleaner too). There will probably still be some rust coloring on the pad, but it shouldn't be enough to cause a problem.
After cleaning, you should really inspect the metal around the pad too to make sure it is not corroded to the point that it may not fit the caliper right or could possibly break.