What a great topic!
As a fan of the show as well as of the wicked one herself - Wilhelmina W. Witchiepoo - I can't imagine a man playing the character. First of all, he would have to have an interesting name such as Winston W. Warlock as I doubt any self-respecting male witch would allow himself to be called "Witchiepoo."
From the time of the earliest fables and fairy tales witches have often been women. It works particularly well in this scenario since Witchiepoo lured Jimmy into the boat. I don’t know that a male witch could pull that off or be as conniving as she was in her best moments. Additionally, it allowed Pufnstuf to be the dominant male hero and protector which also falls into a standard pattern.