She caused an immense amount of deaths to those who were complicit in her torture, those who were simply doing their job, and flat out innocents. She strung you along throughout the entire process, lying to you and promising a solution to a life threatening, and time sensitive, issue. Hell, even if you ignore all of that, her plan leaves you as a target of NUSA if you go through with it. All of that combined with her willingness to push past the Blackwall for her own goals, risking the unknown of that hell.
I don't know if I would consider V a whole lot better considering how the endings play out in the main story, but that doesn't make her own actions excusable. Funnily enough, it was the lying that really pushed it over the edge for me. Both V and Songbird share similar situations of having to tear apart the world in the hope of finding a way to save themselves. But she uses that aspect of V, something she understands well, to manipulate them.
I betrayed her, then mercy killed her and told the president to shove it.