What about having corps/guilds/cults that inflict penalties on other civs while providing them with bonuses that pale in comparison to what the parent civ gets? So the Khazad hate the fact you spread a Death Cult to their city (even though they gain a slight bonus), because they lose a couple points of food, health (or whatever).
In the meantime you gain commerce or something else.
In the meantime you gain commerce or something else.