Ryuko is starting to let Sara act for herself, not much, but a little. Ryuko saying that she believed Sara, and trusted her, didn't mean she trusted him, to Saku, in a way that threatened that if he hurt Sara in anyway, he'd be sorry. Even though Saku is told by Sara that he's a good person, he doesn't really believe her, he was abused and put down by his father so much as a young kid, till he moved out on his own, that he can't not believe anything but that he's a bad person.