I think by now the Halloween witch has become a traditional symbol of Halloween. She's more a pop culture icon than a historical figure, and I think that's okay. People don't like it when you mess with their symbols, though. And she is most definitely a symbol of Halloween at this point.
I don't think it's such a big deal, really. People automatically associate that particular with fantasy and fiction rather than reality, and I think modern Neo-Pagans can sometimes be a little bit oversensitive, taking offense when none was meant. I'm pretty cool with flying halloween witches in cartoons and costumes and decorations.
In fact, I remember the first time I ever viewed a "witch" as a good guy.
I was probably about four or five and I watched this cartoon:
http://youtu.be/skdVouumMk4Summarry: On Halloween night, Donald Duck kind of being a d**k to Huey, Dewey, and Louie on Halloween. He steals their candy and ruins their costumes, hee hee, he is cartoonishly mischievous.
And then this witch comes along named Witch Hazel (ha ha) and she feels bad for the boys and tries to get them their treats back by asking Donald nicely. She appeals to his sense of good and the mischievous but not malevolent spirit of the season. He proceeds to douse her in water as a prank and smash her comically large nose in his doorway.
Witch Hazel is not pleased and takes the boys aside to work some MAGIC, because STEALING CANDY FROM KIDS IS NOT RIGHT, and because nobody touches her nose and lives.
Well, at that point IT IS ON in a matter similar to that of Donkey Kong, as far as Hazel's concerned. She uses SERIOUSLY AWESOME MAGIC POWERS to break into Donald's house where, when he stows the treats in the pantry, she proceeds to do a series of very violently cartoonish things to get him to spit it back out. In the end she makes him run a long way away and then ram the door with his head to get it open. This would probably have killed him in reality, but it's a cartoon, so he was fine. The boys got all the treats they could wish for, and all thanked and hugged Witch Hazel, and she was kind of the hero.
And I remember, in my four year old brain, thinking THAT IS AWESOME.
So not all Halloween witches are evil infulences. ^_-