And, my favorite tool when it comes to thrush is a pick that looks like a "dental tool", but is actually for carving wax. It helps get every last possible nook and craney clean before you scrub and apply 50/50.
Personally, I would not play w "ouchiness", and as others have said I would not ride her until it was completely resolved. If she has thrush, I would treat it, but I would be considering any other possible reasons, too. Did the terrain she is kept on change? Do you ride her on ground that is far harder than her pasture? Her diet, etc.,.