One remedy I find works well on hot spots and sores is the Blue Power Ear Treatment recipe. I've used it on myself as well. And yes, hormones can cause things to go wonky, hopefully it will clear up once her season is over.
Whether it stains depends on the texture of the hair and how long you use it. I find with MOST dogs a single application won't stain the fur, but there are some that will turn blue right away. Long term use gave the inside of Webster's (brown) ears a greyish/purple tint.
Most of my own dogs don't seem to "take" color well, the girls at work tried to color them a couple of times and the various types of coloring just didn't seem to "stick". I can only suggest trying an inconspicuous spot a seeing what happens.
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