I hate to tell you but if the metal has rust bubbles it is going to be through the metal when you clean it up. It would need to be cut out & a patch welded in or get another fender. I would try to patch it, then you have a small area to re-paint. If you replace the fender you will have to paint the fender and blend the paint into the adjacent panels to get a color match.
OR, you could grind the rust out and fill it with body filler. That should hold it for about 6 months.