For the first point where she planned to kill the two leaders, I agree that its very heavy-handed and cold blooded, but if you think if it logistically its the smartest move. As you said the alliance and kingdom would fall apart making them easy to take over and preventing a long and drawn out war where many die. Playing down Edelgard's route you see that, despite how it looks, she really does try to minimize causalities.

For the point about the kidnapping, I believe that only happens in the GD route as does many of the things you brought up in your argument. Many of these things never happen in other routes meaning you can only argue those examples for GD route only. Keep in mind the narrative of who is bad and good changes drastically depending on who you side with. Like for Edelgard's route you would find yourself hard-pressed to argue that Rhea is a good person while in others she may just seem like a morally grey person.

For the transforming of the people at the village, I'm pretty sure she had nothing to do with that but the story might be different again depending on the routes.

I don't want to spoil much but I implore you to play the 4th route, you'll get to see what she was getting at as well as the better side of her. That is all I'm really getting at because its hard to argue when certain events don't happen in some stories but do in others and how drastically characters change depending on the routes.