Through it all, though, Maddie was portrayed as what she was --a victim. Her status as a clone was never used to deny her personhood or render anyone else blameless for what happened to her, it was just one more aspect of the tragedy that was her brief existence. She was made to be used and thrown away, and she ended up exactly that. But she was a person, with full agency and feelings, and her eventual reaction to her situation was a descent into bitterness, nihilism, despair, and revenge. She was a deeply sympathetic character, and Sinister was utterly despicable for what he did to her. And when (usually straight arrow no-kill) Scott killed Sinister, not a single person present objected. And that was in large part because vengeance for Maddie was considered just. Sure, Maddie just tried to kill them all and had turned New York into demon hell, but she was -used-. There was no doubt that Sinister was responsible. Maddie and Scott were just pawns in the game.
That's why I love this story so much, it's like a greek tragedy. Everyone in it is doomed by their own nature, cursed by their fatal flaws. Scott in this was a well-meaning fuckup, who punished himself deeply for his every failing, but who clearly caused a lot of harm in his awkward fumbling. Maddie was an innocent victim who eventually went over the edge from all the abuse she suffered and tried to lash out and destroy everyone around her who had hurt and betrayed her, but in the end destroyed only herself, the one least deserving of it. Jean did nothing wrong per se, but she was much of the motivation behind the tragedy regardless because of others desire for her. Warren's own desire for Jean caused him to do everything but the right thing to help the situation, and he had the opportunity to help prevent the coming tragedy but instead did everything but. Hank and Bobby wanted the old band back together, and sympathized with Scott's pursuit of Jean because it mirrored their own desires for her, and thus they encouraged and enabled Scott to leave Maddie to be not just with Jean, but with them.
Nobody meant anyone to be hurt, much less die, but that's exactly what happened. And they all bear some responsibility. Sinister and Hodge bear the most, because they were manipulating events behind the scenes, but every one of them played their part. None are blameless, depite innocent intentions.
Which is what makes it one of my all-time favorite stories.