We just had a rain rot nightmare at our barn. If the scabs are small, we treated them by scratching them off, then spraying the infected area with 50% diluted yellow Listerine, and rubbing it under the hair.
One mare had bigger scabs, and the Listerine burned because the scabs bled, so we had to bathe her in betadine. We had everyone all cleared up in less than a week.
You can also use homemade skunk stink remover. 1 pint of newly bought Hydrogen Peroxide mixed with a quarter cup of baking soda and a tablespoon of liquid dish soap. Mix it right before you use it, then use it like shampoo on the leg, and rinse off. When the Peroxide hits the baking soda it released a TON of oxygen directly onto the infection. The rain rot infection is anaerobic, which means if you can expose it to oxygen, it dies.
So the keys are get the scabs off to get air to the skin, use something to kill the bacteria, (Listerine, betadine, or deskunker) then keep the hair dry so the skin remains exposed to air. Keep repeating until the scabs no longer reappear.