New pistons would be my automatic response, but the more I think about the JBweld trick, the more I think it might work.
Seems to me that if the JBwelded pistons are carefully smoothed and polished after drying there should be no problem. Assuming, that is, that JBweld doesn't expand or weaken in contact with brake fluid.
I think it's worth a try. If it works, it works, and if it doesn't, the worst possible outcome is probably a system that needs to be completely flushed to get rid of hunks of JBweld, and then fitted with new pistons.