Nah ... there is a big bad.
Yeah, Hayward is the "Big Bad" villain.
Someone somewhere turbo charged Wanda's powers.
Or Wanda, in her grief, just fully tapped into the chaos magic in the universe by accident and is doing all of this on her own like what was shown in the episode.
In the hydra flashback we saw a figure in the mind gem glow (looked like Scarlett Witch) thus narratively separating Wanda from the Scarlett Witch.
Most likely that was just a vision that Wanda had of her being destined to be a "Scarlet Witch".
Plus the book in the basement glowing with magic (from somewhere).
A witch having some magic book in her basement isn't that out of the ordinary and the fact that the only glimpse we got of it was in Ep 7 as part of the camera panning the witchy basement decor and we haven't seen it since seems to me like concrete proof that it doesn't matter to the story being told on this show.
Plus in the flashback they implied Harkness was using magic from a very dangerous hidden-hand source - (i have more to say about this later). That same source killed the other witches. Look at the scene again. Agnes was surprised when the purple magic started to fight back against the coven.
Yeah, Agatha's mom told her she was messing with dark magic she wasn't supposed to be touching. And the surprise was basically her being a young untrained witch who assumed she was going to die but was so much more powerful than the rest of the coven that she siphoned their magic instead.
You are making a huge assumption that it was some singular source who was controlling what was going on instead of Agatha just using dark magic the same way Wanda is using chaos magic. Like how The Ancient One was using magic from The Dark Dimension but wasn't being controlled/manipulated by Dormammu.
One other thing is "coven". in the flashback the witches spoke as if covens were the norm. anges never said that there are only two of them in the present.
If there are still existing witches covens in the MCU it wouldn't be some shocking thing. It also doesn't mean that it has anything to do with the story being told on this show.
One other other thing in general is that Agnes never actually did anything evil so do not assume that she is the "villain". If anything she seems to think Wanda is the danger hinting that she has room to develop into a Loki type.
We also were pretty much told that Agatha was an innately powerful witch who was dipping into magic she wasn't ready or trained to be touching. So the gist of it looks like Agatha is big into gaining new magical power and she spent the bulk of the season manipulating Wanda to try and find out what Wanda's magic source was so she could get some of it for herself. Once she realized that Wanda was using chaos magic she realized how dangerous Wanda was because Wanda is doing insanely powerful magic stuff without even realizing it.
So I agree that she's probably going to end up as that tweener character like Loki because when she realized what Wanda was doing to Westview she didn't try to stop her or help the people under Wanda's spell...Agatha instead was working overtime trying to get Wanda's power source for herself.