This is where playing as a Sith comes in handy. You can Punish your companion at your whim. "Why can't you be more like Lana, Ashara? Now you'll pay for your insolence!"
Aw, it's more subtle with a Jedi. "You say you care about me, Qyzen? Alas, I cannot experience anything towards you. Wait... Wait.... Nope. Not a thing. May the Force---"
But yes, it would be great if you could recruit NPCs and throw out certain other undesirables.
Unfortunately, the way Affection is tied into the game mechanics it will make things awfully difficult and open things to abuse. Getting rid of the companions, as probably was mentioned earlier, was an available option, but interfered with the game badly, and caused a swarm of complaints.