I recently read that gentian violet has been linked to cancer (although these days, what isn't?).
I have had success treating mild to moderate thrush by doing the following - scrubbing the hooves with a stiff brush (like the brush on the back of a hoof pick) and regular dish soap (dawn or ivory) and rinsing thoroughly. Then spraying or pouring on 50/50 apple cider vinegar and water solution. Followed by some iodine (which can be harsh, use your judgement) and then pack the thrushy areas with desetin diaper cream. No, I'm not kidding. Since the hooves are clean and treated, the diaper cream keeps moisture and gunk from getting in there. Repeat every other day or so until the thrush is gone.
Another thing that works well is making a "goo" out of neosporin + pain releif (or the generic equivalent) and 1% clotrimazole athlete's foot cream, put this into one of the curved tip "monoject" syringes (you can get them at a tack or vet supply store) and put this as deeply into the thrushy area as possible. After picking the hooves out, of course.
I am also a BIG believer in ToDAY cow mastitis treatment. It is clearing up a bad (as in bleeding) case of thrush in my recently acquired gelding.
The most important thing is to KEEP treating it, and do it consistantly. Don't do it for 3 or 4 days and then go a week before treating it again. Get the thrush GONE.