Rather than killing the antagonist or having her sent to some kind of special prison, Wanda opts to leave her in the state in which audiences first met her – which is to say as a nosy neighbor living in Westview, New Jersey.
This is definitely a more open-ended conclusion than most villains get in the franchise, so it will be interesting to see if this is really the last we see of her in the canon.
Before she can totally drain Scarlet Witch of her magic, Agatha finds herself unable to cast spells due to runes that the titular heroine places on the walls of her hex, and this leaves her totally helpless.
Agatha Harkness’ quest to harness more magical energy in WandaVision leads her to do some pretty terrible things, including killing a dog and kidnapping children… but being evil doesn’t typically play in the Marvel Cinematic Universe, and in “The Series Finale” she winds up getting her comeuppance and suffering a rather disturbing fate.