Plenty of the light side options for Imperials have nothing to do with Yin/Yan, Black/White, Good v Evil, philosophy or the Force. You're rewarded simply for assisting the empire. Assisting Nekghouls helped empire via depriving the Republic of a potential ally. BT is the same way. Light side choice is him getting tortured not because you're preserving life but because the Empire wants to torture him and learn whatever bit info they can.
Very stupid I know. As a light side Sith Inquisitor my storyline should be about not caring about or even actively changing/demolishing the Empire from within. Earlier quests supported this idea. . By Tatooine, "Its long live the Empire". Hopefully any expansions have a more cohesive story experience.