Peter if the new pads are going to rub on the lower edge where rust is then I would take some wet and dry paper to them to clean the area up using even pressure whilst spinning the disks. I would start with 800 grade and see how they come up. You don't need them polished as the pads will do the final job, just remove the loose rust. I would do this to ensure the pads don't initially grab on the rust, when you first use them.
