Once the bearings have become rusty, they can be cleaned but they will never be as 'good-as-new'. Soaking the bearing in penetrating oil (WD-40) is a good start, but in reality all you are doing is squeezing a little more life out of the bearings. The effects of rust are irreversible, the oxidized steel is no longer there. The balls and races will be pitted, the balls will be slightly out-of-round, all because the metal that was there is has rusted and flushed out by the oil.
Don't get me wrong, I've brought trackballs back to life that were completely frozen up too, but they are just never as smooth as they would be with new bearings. And once corrosion has set in, then it is more prone to start rusting again so you may have to lubricate the bearings more often than normal to keep it running as smooth as possible.