This is the MCU, they have set the precedent that sorcerers & witches are their own thing, not mutants. This episode only further emphasized that Wanda is a witch and not a mutant. I would never consider Thor a mutant, he's the god of thunder. Skrulls are aliens from across the galaxy, not mutants. And now, in the MCU specifically, sorcerers & witches are not mutants.
You are saying "sorcerers & witches are not mutants", I am saying "sorcerers & witches
can be mutants". Not all mutants are sorcerers, not all sorcerers are mutants, but being a mutant can manifest in thousands of ways, one of which is by giving the mutant magic abilities, thus making them a sorcerer. Because what a 'sorcerer' is, it's just a fancy word for 'person who can use magic', and magic is just a thing that exists in the world. There are multiple ways for someone to use magic.
Instead of 'sorcerer', allow me to use the synonym 'magic-user' and make a comparison with 'fire-user'.
Fire is a thing that exists in the world. People can have the ability to use fire in various ways. We define a
fire-user as any person who has some ability to create or manipulate fire.
A
fire-user can be a person who has learned the mechanics required to create or manipulate fire. We'll call this a
learned fire-user. This is a very broad term that encompasses all levels of fire-usage. Anyone that knows some application that combines the components of fuel, oxygen and heat to do something with fire falls in this category. This could be a caveman that has the basic knowledge and skill for banging flint to get sparks that can light dried grass. It could be a trained fire fighter who has learned specific skills to control fire for a specific purpose. It could be a physicist who knows all the formulas and theories and the autoignition temperatures for different materials, etc. and can create all kinds of stuff like colored flames and fire tornados in a controlled environment.
In the MCU, a
fire-user could also be someone with an innate ability to use fire. We will call these people
innate fire-users. An example would be the fire demon Surtur. Surtur didn't have to learn any of the techniques a learned fire-user did. He
is fire. He can just use fire however he likes and didn't have to study for it. He can even seemingly create fire without requiring any fuel and generate heat himself, thus giving him more ability to use fire than most learned fire-users. It's also possible to become an
innate fire-user rather than be born one. Someone who could fall in that category could be Scorch from Agents of SHIELD, who developed innate fire powers at some point possibly from a fire at a nuclear power plant near his home.
Now, we can imagine that the X-gene (aka being a mutant) can create a
fire-user, specifically someone with the X-gene would have an innate ability and thus be considered an
innate fire-user, though obviously not every
innate fire-user is a mutant because Surtur for example is not a mutant. We will specify this special case of
innate fire-user to be known as a
mutant fire-user. This would include any mutant with fire abilities, such as Pyro, Firestar, Sunfire and Sunspot. Though of course these people could still learn other uses of fire too, such as Pyro using lighters and flamethrowers as well.
Now let's apply that same logic to magic:
magic is a thing that exists in the world. People can have the ability to use magic in various ways. We define a
magic-user as any person who has some ability to use magic.
A
magic-user can be a person who has learned the mechanics required to use magic. We'll call this a
learned magic-user. Anyone that has learnt some ritual that combines components to create a magical effect or an application of such falls in this category. Compared to fire this is a bit more complicated than fuel+oxygen+heat, but it could be something like sling-ring+hand movement+specific thoughts and belief. This could be someone who only uses a single magical effect, such as Jonathan Pangborn, or someone who tries to master them all, like Doctor Strange. It is implied that magic is something that can be learned by anyone, though some may have more talent or affinity for it.
A
magic-user could also be someone with the innate ability to use magic. We will call these people
innate magic-users. This would include beings like Dormammu who simply
are magic and didn't have to learn their magic like people in the learned magic-user category. Another example might be Daimon and Ana Helstrom who have some presumably magical abilities such as exorcism, vitality absorbtion, psychometry, etc. as a result of being part demon.
Now, we can imagine that the X-gene (aka being a mutant) can create a
magic-user, specifically someone with the X-gene would have an innate ability and thus be considered an
innate magic-user, though obviously not every
innate magic-user is a mutant for the same reason given for innate fire-users. We will specify this special case of
innate magic-user to be known as a
mutant magic-user. This would include any mutant with magical abilities. Examples from the comics would be Wiccan, Pixie, Magik and at one point Scarlet Witch until a later retcon. It should be noted that like how Pyro also utilizes learned fire-use, most of these combine their innate ability with additional learned magic-use
Now, what category are Agatha and Wanda in this show?
For Agatha we don't know the origin, but we do have a clue. At the start of the episode she is surprised Wanda doesn't know about basic protection spells that one would learn early when learning magic. This implies Agatha would fall into the category of
learned magic-users.
Wanda on the other hand, is said to already have had something in her. She never learned the basic spells because she never learned magic, she just had it. It is said she already had something before her interaction with the mind stone, and that something allowed her to survive the exposure to the mind stone and was subsequently enhanced by it. This would make Wanda an
innate magic-user, unlike Strange or Agatha. Now, is she a
mutant magic-user? We don't know. She could be, or her magic could be some other innate thing like magical blood passed down generations or altered genes because of interference by the High Evolutionary or whatever. The point is, people are thinking Wanda might be a mutant because she's clearly special. She had this ability innately, unlike Agatha who was surprised she never learned the basics despite being one of the most powerful magic-users and unlike Strange who was just a talented regular guy who studied magic really hard.