But you have absolutely no idea, why he is doing this. You don't know if he (or the player) is being mind controlled somehow. For all you know the player could be running around with a bomb in there head and Theron is cooperating to not make you go "boom". (not saying this is the case). Just look at the entire Imperial Agent story line. If they had been a companion, would you have murdered them too?
Again, you can do whatever the game allows you too, but killing a companion based on a bunch of assumptions, when he is so obviously still on your side, seems a bit extreme.