Kaku will have reformed - after the fight with Zoro, he realized he didn't really want to be an assassin anymore. Lucci might become more appreciative of his fellow CP9 members.. no idea about the others, though.
If anything else, I foresee CP9 becoming the Anti-Strawhat force in the story now. Basically the enemy they usually need to work hard on beating (i.e. CP9 will get upgrades!).