The rewrights in the game are awful so you make the mutant girl the bad peson in the scenario and you have to side with him if you're a good person. You do the same thing with decayed "granted she was always the bad guy" {also cutting out the flirting with Shani during the decision process} but putting the decision before the storm rather then result of storm makes taking her make you into an even worse person. And side with the mutant if you're a bad guy?" Making her a non-slave doesn't phone home how the Zeton way is as well might makes right which is a staple of their entire infostructure and culture
"Might makes right, I can do whatever I want with my property!" Douchbag says "Prepare to defend your property" Zaton replies with one of the hardess lines in the game. Not to mention he was beating her for food cooked terribly not biting his damn hand off.
Maybe it's because I am about to hit the bed but I barely understood your complains, my bad. However, there's some misunderstanding in this "bad guy-good guy". I think that's against the philosophy of the game. Those are conventional values which, in it's theme, the game is trying to reject (poorly but that's a very complicated goal).
I don't think there are evil or good choices in the game. Some choices are more oriented to protect others while others are there to increase your strength as leader. You are a tyrant anyway, the difference is, if you think of others more or less.
It's like they did in mass effect. Shepard is always the same character. The renegade one will go "beyond" in some situations, ignoring lateral damage caused to other people, but the guy is still saving the galaxy. In the final balance of the universe, Shepard would still be a good guy. Zaton may be more or less compasionate but that doesn't change his main motivation: To protect and expand his family. It's the same no matter what.