Not having read most of the post (I don't want spoilers since I'm just a lvl 20 Sage right now), but I have no problem with Qyzen. He doesn't like you coddling people, he likes when you have people help themselves or at least check to see if they did something before offering your help. I've gotten negative from him by say "I'll help you" when there was an offer of "What have you done so far?" So I'm learning to not just rush to fix things but try to lift people up so that they have the strength to carry on. I've pretty much taken the light side options on most quests and his affection for me is quite high. I compare this to the Inquisitor I play where Chem Val disapproves of anything I say because I respect my master and support the Sith. Sure I make up affection by being a cruel person and like fighting, but I groan or send him away anytime I enter a quest dialogue that involves the Sith. Same with my Agent, Kaliyo seems to disapprove of many things I do because I'm a staunch Imperial. Any show of support for the Empire and I see that frowny little -1 from her. Give her a weapon gift though and I do see 100+ positive score. Compare that to my Smuggler. Me and Corso get along like best buds because being a happy-go-lucky smuggler that likes to help people fits well with his demeanor, I don't think I've ever seen a negative score from him except when I executed some Imperial guy. That's been a little fun game with me, seeing how I can play my character the way I want and work within the constraints of a judging companion.