I agree and disagree. I agree that when such a belief is used to enact such extreme punishments of reprehensible nature, the law itself needs to be debated and hopefully amended. I do not believe however that it makes the original belief itself second rate. Just because some Right Wing crazy judge abused the system to get at the belief, doesn't mean those in Saudi who hate witchcraft are suddenly all cruel.You are correct, a belief in witchcraft is not bad, in and of itself. When that belief is used to punish people without evidence of wrongdoing and harm, then it becomes a second rate belief, at best.
I'd imagine the judge did this to send a wider message anyway. As in, haven't done one of these in a while, let's send out another message that witchcraft will not be tolerated. Doesn't make it any less reprehensible but I'm assuming that was the thinking behind it.