I do not kill companions just because I disagree with them about ethics (or anything else, really). It's their life to live, not mine (man, how often did I use that sentence in RL debates lately). If they did something I can't tolerate, I'd still prefer to go separate ways rather than kill them.
Having said that, if things turn out, by the way I navigate the plot, that we end up on opposite sides, then that's too bad. I'd like to come to know Minthara, but since I won't side with the goblins as a rule she'll likely end up dead almost every time.
Everyone else, I hope to keep alive.
careful about being too tolerant though...in this game ALL companions are particularly dangerous and they aren't mindless drones following you. They all have plans and schemes...follow them blindly or just be too nice and unquestioning and you'll probably end up dead. One is a vampire, one was one of the most powerful archmages in existence who romanced and betrayed the goddess of magic, one is on a very important quest directly in service for the goddess of secrets and dark magic, etc. etc. etc. Let your guard down or just follow someone without questioning and you'll probably end up in over your head. They are all very VERY dangerous people.
I'm tolerant, not stupid. The Githyanki think they're the master race and Lae'zel is typical, so I did not go to the Githyanki with her in my first playthrough until I'd tried everything else, on the rationale that they might think it's easier to just kill me to get rid of the mindworm infestation. I certainly did not react favorably to Gale's advances even though we're both arcane spellcasters, and I won't kill half the druid grove just to get him that statue of Silvanus.
So it's possible I'll get into an irreconcilable conflict with some. But you know, I don't want mindless followers, I want as companions dangerous people with minds of their own.
