What she knows about death is immaterial; she's so singular in her purpose that I doubt a personal understanding of death would change her actions, and she has to at least have understood the significance we assign it given how well-developed her ability to empathize and interact with humans was.
But I don't think this is really about whether she has evil intent as much as her role in the series. She's a potent antagonist who menaces the main character, so calling her a villain seems appropriate even if she doesn't act out of malice.
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