The person now known as Beatrice, perhaps romantically, perhaps maternally, loved Battler. Then, six years before the events of the game, he told her that he did not return her affections (don't blame him, he's only twelve at the time).
As the saying goes, hell hath no fury like a woman scorned. At that point, whoever the person was before, that part of them "died" after they took on the title of Beatrice the Golden Witch.
Or, if you want to try to figure out the supernatural aspects of the games, perhaps she literally died (somehow Battler's fault) and became a ghost who haunts the island. Battler and the others cannot see her in the first episode because, as has been stated several times, you cannot see the magic without love, and he did not have any love for her, whereas the servants revered yet feared her. Kinzo regarding her as a love interest is irrelevant, as he is dead at the beginning of each episode.
If the ghost theory is correct, then it explains why Battler can see Beatrice in Purgatorio, as both of them are dead (or "mostly dead", at least) after the end of the first game. Come to think of it, saying "a ghost did it" is not the same as saying "a witch did it" and could explain the locked rooms if your view is more anti-mystery. This also explains the "Black Witch" as being a malicious spirit that has possessed one of the relatives (like Rosa, for instance).
Then, building on the possession theory, the crimes Beatrice says "were not committed by humans, etc." were instances where she or perhaps her servants possessed a person or at the very least strongly influenced them into committing the murders (like Kasumi at the end of episode four). Thus Beatrice could say it was/was not committed by humans because it's only half true.
I've strayed from my original theory, I know, but all of the other stuff came to me as I was typing
Feel free to poke holes in it.