Well, I started out going all-out dark on my Bounty Hunter, but then I got Mako as a companion. I don't know why, but I started picking the choices that Mako would like (light-side choices). Maybe I did this because whenever I would walk up to Mako she would be all like, "Hey girl! Let's make some easy credits!" I would just think: "Hm....money sure can bring cyborgs together. I like this kid".
I know, it's weird. But honestly, I had no more fun being Mrs. I'm-gonna-chop-your-head-off Bounty Hunter than Mrs. I'll-just-leave-you-alive-but-stll-turn-you-in-for-credits Bounty Hunter.
All in all, I'd say do what you feel is right, but don't rack up negative affection with your companion. That's what works for me, anyway.