I've got to sort of agree with the Kaliyo thing. Although I was fine with her coming aboard, I started to get a bit annoyed with her when she took a dislike to my loyalty to the Empire. When the end of her companion storyline arc, IC my character would have eliminated her there and then. Unfortunately I knew I was stuck with her, so I gave her the "we have to work together" speech. I still would have taken her, but the death option would have been appreciated at that point.
I'm suprised when I've had a few options being against the Empire, gave me a negative reaction from Mako.