Anyway, I can imagine what the best possible social organization for defeating chaos would look like.
Basically, just do the exact opposite of the Imperium of Man in almost every regard. Create a just and free state that tries to maximize the happiness and contentment of all citizens. Encourage the welcoming of the different and alien. Eliminate want to the best of your ability.
Chaos is invited and empowered by conflict and desperation. Produce less of those emotional energies, and the chaos gods will have fewer opportunities to exploit, their power will weaken, and some new and more benign gods are likely to form eventually. The Imperium is constantly at war with everyone else and itself (feeding rivers and rivers of blood to Khorne), and forcing quadrillions of sentient beings to become desperate (feeding Tzeench), give in to despair and apathy (feeding Nurgle), or decide to drown their misery in catharsis (feeding Slaanesh). The Imperium of Man is the foundation on which Chaos is built. The soil from which it draws nutrients. Smaller societies are probably only getting overrun by chaos BECAUSE of the Imperium's emotional pollution of the warp making chaos stronger.
It's probably too late for the Imperium of Man to turn itself around. But that's not what the OP is asking. The Imperium isn't humanity's one reprieve from chaos corruption, it is one of the two MAIN SOURCES of chaos corruption along with the Eldar Empire and its Drukhari survivors.