Ugh so frustrating. I had a tea tree oil spray that worked amazingly well on rain rot but I can't remember the name. I rarely had to use it on mine. I just used it on a mare who tended to get irritation and skin infections on her heels and fetlocks. One day at a show though someone asked me how to cover up a bad patch of rain rot on their horse. I had no idea but I did have a way to heal it. I sprayed the horse, shrugged my shoulders at trying to hiding the patch of thin hair and damaged skin, and walked off thinking that was that. 3 days later I get a call. The skin is nearly completely healed and the hair is growing back quickly. They are dying to know what it was I sprayed on their horse. Now I can't remember the name or find it!
I tried all the bottled stuff and it would take so long for it to clear up so I started using diluted bleach water. Works 3 times as fast as the medicated stuff.
Make sure you brush her good, get all those clumps off and spray the area with bleach water. Works like a charm. I won't use anything else anymore. I know it isn't the natural remedy you are looking for but it really works good.