I wouldn’t agree with the assessment of the main characters being a-holes. Maybe in the carefully cut clips devoid of the full context.
In the first scenes, the protagonist is indeed somewhat mean to her crew, but the game immediately tells you as much, to show you that abusing the special abilities, Vox, is not a good idea. From there, it’s up to the player whether to listen to every dialogue to the end or to interrupt, whether to avoid using the charged Vocals or to use them frequently. Going by the post-chapter stats at the end of one particular chapter, most players choose to avoid them at least in that instance.
Short of the introductory scenes that teach you to avoid using the special abilities, I can’t think of a case of the protagonist being manipulative in a negative way. It’s worth noting that she can be as bad as the player though, if they decide to interrupt people and use her powers to the same end.
To your second point, there are enough examples of Justice being bad, like their officers talking about arresting people purely out of being annoyed, being kinda racist (e.g. saying that two Black individuals must be siblings, then to themselves wondering if that’s racist), going after a little girl for having special powers, experimenting on people, persecuting all people with special powers and regularly calling them deviants (all while claiming to promote diversity), trying to arrest peaceful protesters, and so on.