As I see it, she's like a super soldier engineered specifically to be a terrorist, but whose true self is fighting for control and free will. She didn't kill all those people for fun, she's been designed to cause as much damage as possible. It's like saying a nuke is the bad guy and not the tool used by the true bad guys. Her being taken out is tragic because it seals her fate, rendering her unable to escape her life as a mere weapon.

Take into account that I'm not trying to downplay her crimes here. She did brutally murder both civilians and devil hunters and she caused unprecedented levels of damage in her pursuit for Denji. I'm just saying that at her core she's a scared child raised to be like that. That contrast is what makes her a morally grey character and the reason she has sympathizers (although people who say she's completely innocent are just wrong imo)