This is an interesting topic. I completely take your point, but I came of age at a time when the archetype of "the witch" was being remade as something more positive in children's fiction, so that's my first association.
"Witch" books that spring to mind immediately:
- Meg and Mog, rhyming picture books I loved as a baby
- Witch Child, by Celia Rees (a historical YA novel focusing on the Salem witch trials)
- The Tiffany Aching Discworld novels by Terry Pratchett.
- Serafina Pekkala and the witches who rescue Lyra in His Dark Materials.
There were, of course, older books where "the wicked witch" did appear as a trope. The Narnia books are an obvious one, and the Roald Dahl book "The Witches".
I have mixed feelings about the latter. While I don't think Dahl went out of his way to write a feminist book (far from it) I do think he unwittingly does some positive things with it. I like that the boy's grandmother (a rather unfeminine old woman) is the hero of the story. Her intelligence and observance, her ability to love and reassure her grandson even when he is turned into a mouse, and her refusal to give up even when the system seems so rigged against her and she can't even be taken seriously if she tries to name the problem . . . all this exemplifies the "women's wisdom" and courage I imagine real life witches possessed.
Reading it as a child, I also found the witches thrilling, I'll admit. I enjoyed reading the gleeful depictions of their ugliness, in a era when women are supposed to be beautiful above all else. I enjoyed that the falseness of that was shown - that the books challenge the idea that beautiful = good. And it was a little bit thrilling to read about this secret network of women who hated children and motherhood, and were free to be as nasty as they wanted about it in private. I enjoyed them immensely. Yes, they got their comeuppance, but in my young eyes they had taken it a step too far into the realms of actual child killing, so . . . shrugs They were my favourite Dahl villains, way better than the boring male giants in the BFG. The witches had DIMENSION, as did the evil old grandma I'm George's Marvellous Medicine, and Trunchbull in Matilda. I loved them as a kid, and felt they gave the stories all their fun.
Similarly, I really enjoyed Jadis (the White Witch) in The Magicians Nephew. Yes, she was a bully, but she was primarily bullying Diggory's patriarchal, bullying old uncle, and it was very satisfying to watch him get a taste of his own medicine. I also enjoyed that the witch couldn't be fully defeated at the end of the novel. She was something older and more unknowable than Narnia itself, and would always be a part of the world. (Yes, she was being used as a metaphor for evil, but the unintended consequence was that Lewis wrote this powerful, indefeatable woman into the very foundations of the world. I read it as a child and felt really excited by the idea that she'd always be back, like the Terminator. 
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