I think there are a couple of flawed premises in your question.

First, "witch hunts" are really an Early Modern thing, not something from the Middle Ages. They don't really start up until the 15th century. The Malleus Maleficarum, which famously mentions red hair as a possible sign of witchcraft, didn't really have the authority people imagine it had. The Church condemned it, and it appears to have been used more by secular courts.

I can't think of a single account of someone actually being prosecuted as a witch because they had red hair, though I'm a medievalist, so there might be some Early Modern accounts I'm unaware of, but I kind of doubt it.

Plus, red hair was just one sign of witchcraft, along with a variety of other witch marks. Redheads appear to have gotten along just fine. Heck, Elizabeth I had red hair, and she seems to have done OK for herself.

tldr These witch hunts for people with red hair are more about our popular imagination than actual practice.