Bead blast would be good, as long as you clean it good afterwards to get the media off.
If it was mine, I would use Alumibrite (truck wash) & make a soak tub & let it sit in that most of a day to eat the rust off, then oil it up good to keep from rusting again.
Most important part in it all, is cleaning those threads in the center of that flywheel where you would screw in the puller, because rust can mess them up & then the puller is no good because the threads are rusted away.
Its always good after a ride, to pull the ignition cover off & a good soaking of WD 40 all over the ignition, soak the whole area with oil.
Next, would be a small drain hole in the bottom of that ignition cover so the water can get out.
Neil