I have quite a good solution to killing off companions. You get to kill them, and then you get a replacement for them in the form of a generic companion. For example, if you kill Quinn, you get an "Imperial Agent" who functionally identical, but you get no dialogue or story options with him. Therefore, the decision to kill quinn will only impact your story. I am surprised nobody at Bioware thought up this solution.
*runs off to hug her Quinn "It's okay, snuggle-bunny, an IA could never replace you."*
It would be nice to have those options, probably when they release more companions BW might bring back the option to kill or atleast release those companions you are less than fond of. Me, I like my backstabbie, traitorous Quinn who may or may not actually be loyal to me now that Darth Baras is dead.