This is my biggest problem with the finale. She clearly is a witch serial killer, it's not even just seems like. And I've seen some people who like that she's still obviously a bad person and wasn't magically transformed into a hero against the character's intention. And I can see that, too.
But for it to work properly I really feel like we needed more context of where the hell that came from before Billy just accepts her and moves on. The Nicholas Scratch stuff was great and added great context to Agatha's relationship to Billy to boot, but it only tells half the story of why Agatha is the way she is.
I think the finale really needed another 10 or 15 minutes at the start to show us what the hell actually happened with Death and/or Agatha's Mom/original coven so that we better understand why she had already chosen to be so cynically untrusting that she'd rather just kill people and take their stuff than give them a chance, rather than just giving us her barefoot and pregnant in the woods and already on that path before we meet her.
It does sort of end like in Wandavision. Despite her enslaving a whole town, you are suppose to feel bad for at the end because of the loss of her family and because we clearly come into the show liking the character from the previous movies. In this show we are suppose to give Agatha a break from the serial witch killing because she is the main character and she can be funny with a quirky personality. I can go with it though since Billy is someone who is feeling guilty over get the other characters killed by creating the Witches Road. Billy is not exactly a hero at the end of this story. He is someone who has simply come to terms with who he is and someone with a goal in finding his brother.