Mario Bava’s La maschera del demonio, or Black Sunday as it’s known in the US. And doesn’t the TV series Salem represent witches as a thoroughly bad lot, fully deserving of being burnt? (Although I only caught the first few episodes).
Wait! Wasn’t that the hokey one where all the witches burst into flame with acting so bad even Lucille Ball would have said, “Waaaaaaaa…!” 
In Sleeping Beauty there were three good witches/fairies who tried to protect her, besides the evil Maleficent.
The other two have a single evil witch, but that doesn’t imply that all witches must be bad. She’s killed (in both cases accidentally) because she’s done bad things to the heroine, not just because she’s a witch.
Great movie, when the hero’s best friend, badly injured from a car crash and dying from a dagger in his back, grabs a cross and staggering as he walks, burns the witches before the clock is finished.
Also known as "City of the Dead"
iirc the old Boris Karloff movie Black Sabbath
Tell me, friend, do you get worked up when Blade stakes up a vampire nightclub, too? 
In any case, that’s precisely the reason why I’m asking, because it seems so unusual—although, by a few examples in this thread, not actually unique.
I saw it when I was 9 or 10 on the Channel 5 Creature Feature. I’m sure it WAS as awful as you remember, but I was so young when I saw it, I wouldn’t have recognized a hokey script or terrible acting.
I’ve never seen any of the Blade movies and I’m not worked up about anything. I’m just trying to figure out what you’re asking here. I would have considered The Wizard of Oz a classic example of a movie where killing witches is depicted as a good thing, but you explicitly excluded that one in your OP because Dorothy only kills the wicked witches.
So you are asking for movies where it’s portrayed as a good thing to kill witches regardless of whether they’re actually dangerous or have done anything wrong? There are movies where all witches are portrayed as evil and therefore dangerous, but a movie about how heroic it is to kill old ladies is going to be a tough sell unless it’s clear they’re a real threat.
I think you have the wrong Karloff movie. Black Sabbath had the three stories hosted by Karloff (Boris the vampire terrorizes his family, woman terrorized by guy on the phone who won’t stay dead, dead woman terrorizes ring-stealer [they may have hinted the dead woman was a witch–that one STILL gets me; that dead woman was SOOO ugly]). If you’re thinking REALLY old, maybe The Black Cat with Karloff and Lugosi; Boris was supposed to be a witch. I could be confusing this last with The Raven (1935).
Fairies are not witches in that movie :dubious:
Oh, ferchrissakes. He’s asking for movies where witches are always evil.
Wait! Isn’t Black Sunday where Robert Shaw shoots down a coven of witches flying blimps over the Super Bowl? 
Well Dorothy was kind of manipulated into the conflict by that masterful manipulator Glinda, which is the only reason the Wicked Witch cares about a country girl from Kansas.
Is he? I am honestly not trying to be pedantic here, I really cannot tell from the OP what sorts of movies he’s looking for. The response I got when I asked didn’t shed any new light onto it for me. (Maybe if I’d seen Blade I’d get it, but I haven’t.) A movie where all witches are evil would presumably have witches as the antagonists, but he said in the OP that this wasn’t what he wanted.
You seem to be thrown by this line:
He wants movies where witches are antagonists because they are witches - where being a witch is an inherently immoral state. The Wicked Witch isn’t wicked because she’s a witch, she’s wicked and she’s a witch. She’s the antagonist because she wants to rule Oz, but her desire to rule Oz isn’t directly related to her being a witch: her sister is also a witch, but is a good person. By contrast, in something like Warlock, the movie I mentioned above, a witch is by definition a person who worships Satan in exchange for magical power. He’s the antagonist in that film because, as a witch, he’s trying to free Satan from Hell, which will be the start of Armageddon.
I remember a movie called “Blood on Satan’s Claw”. Townsfolk killed a bunch of witch wanna-bes. Don’t remember if they actually had witchy powers or if it was just an excuse to go lord of the flies on folks they didn’t like and have lots of sex.
Chronicles of Narnia doesn’t have many witches, but it is definitely a world where being a witch is automatically evil.
I am being nitpicky now, but the Wicked Witch of the West’s sister was the similarly wicked Witch of the East. (The one crushed by Dorothy’s house.) Glinda was apparently no relation.
I’m not the first to point out that Glinda is arguably even worse than the two witches labeled as “wicked” – she could have helped Dorothy to return to Kansas the moment they met, but instead sent her off on a wild goose chase that resulted in the convenient disappearance of the Wizard of Oz and the death of the last of Glinda’s witchy rivals – but she is overtly portrayed as being good in the movie.
For clarification, strictly speaking, I’m asking about movies where the practice of organized witch hunting/killing is unequivocally a “good thing”—implicitly, one imagines, this would probably be in a setting where “being a witch is an inherently immoral state.”
So, like Miller notes, The Wizard of Oz doesn’t count because a) the Wicked Witch is being hunted because she’s the villain, who happens to be a witch, not merely because she’s a witch, and b) at least some witches are good, and on the heroes’ side.
Warlock, on the other hand, does count, as it features a professional witch hunter as a hero, and totally “in the right”—and witches, in that movie’s universe, are by definition evil and dangerous. Which you’d think would be the logical prerequisite for such a scenario, but it’s not strictly required.
I mean, it would more more difficult, thematically unsettling, bad storytelling, or even societally “problematic” to do a story where the witches were by all appearances benign, but that slaughtering them for just existing was still depicted unironically as “good”—but I’ve seen a great many movies with uncomfortable, stupid, or deranged themes in my time. Nothing would entirely surprise me.
The best example I can think of has already been mentioned by Sattua, the movie version of the Roald Dahl book The Witches. The story involves an orphaned boy who lives with his grandmother, and they wind up staying at a resort at the same time as a sort of national conference for witches. After discovering the witches’ evil plan, which involves a magic potion that can: turn people into micethe main characters manage to defeat the witches by using the potion on them. In the end the boy and his grandmother make a plan to track down witches in other countries, use the potion on them, and kill them. I’m actually not 100% sure the “and kill them” bit made it into the movie, but that’s definitely how the book ends. In the book the grandmother is also a retired witch-hunter, although I can’t remember if this is stated in the movie. Anyway, it’s clear that the boy and his grandmother are good people and that destroying all the witches in the world is the right thing to do.
It’s probably significant that in The Witches, witches aren’t humans who use magic. They’re a type of demon or ogre that can disguise themselves as humans. These witches are by nature the enemies of humans, so there’s no possibility that a witch could be good or harmless by human standards.