Granted, I haven't played many RPGs, but this reads like a subversion of standard companion design. In the RPGs I've played, the only difference between a paladin who has sworn an oath to complete your mission and a thug who was kicked out of the thieves guild for grand scumbaggery and not paying his dues is... flavor text. They act the same. They stick with you no matter the danger, until you finish the mission. You can always trust that companion to be there no matter what he says.
The biggest subversion I can think of is Wrex in the first Mass Effect game, who can turn on you if you rush through the game and not do his loyalty mission. Mass Effect 2 also has the option of companions being taken out of the game, but that's true for everybody. The crewmates who were there when you took down Sovereign are just as loyal or disloyal as the psychotic lab experiment with a hateboner for your sponsor organization.
Oh, yeah, Original War did it too. That was pretty neat.
A game where you have to think about your companions' motives in order to keep them loyal would be pretty good, especially if there are curveballs thrown at you.
One companion is your standard RPG companion. He stays with you no matter what, and he will be extra loyal if you do his mission. Probably should be a few of these. Just so that the game isn't full of bastards.
Another companion is a Paladin, and though he is sworn to slay the dark lord, he will leave you if you cross too many lines and fail the come-to-Jesus moment.
A third companion is a thief who vanishes into the shadows whenever the fighting in a mission gets too intense. As the game goes on, he gets second thoughts about the quest, and disappears with a lot of loot. The only way to keep his loyalty is to betray him and hold blackmail over his head.
A fourth companion is a swordsman from a desert tribe who swears he will fight the Dark Lord if you free his tribe from bondage, but he also often quotes that "Me against my brother, me and my brother against the outsider" phrase. If you don't complete that sidequest, he abandons you... but he also abandons you if you free his tribe. He got what he wanted, and if you push him to honor his word, the whole clan will attack you. The only way to keep him is if you do his loyalty mission and fail, so that he swears revenge for his lost kin.
The fifth companion is a sorceress who sees the world in power dynamics. This is a poor justification for the fact that she is power-thirsty. She will betray you to become the Dark Lord's apprentice. You need to talk her out of her worldview *and* shield her from a lot of temptation to keep her loyalty.