In MGS the 'weak, corrupt, conniving civilians" are almost always the intelligence agencies of various nations. Big Boss generally doesn't rail against a corrupt civilian bureaucracy that won't let him win the war, the enemies are usually intelligence agencies and special forces groups that manipulate soldiers in to dying for causes that don't benefit them. Like the game manages to portray this bizarre hero warlord without making him a fascist.

Big Boss is kind of a foil to fascism in some ways. He really, truly believes that all people (which in his world is just soldiers and spooks) are essentially equal, that human life is valuable (the game strongly encourages non-lethal methods without requiring them), and that governments should be honest, transparent, and responsive to their constituents (his chief reason for forming Outer Heaven is his belief that soldiers are mistreated and then abandonded by the powers they serve). Of course it's all weird and fucky because he creates a sort of anti-utopian military state, but Kojima never has the protagonists launch in to tirades about how soldiers should run civilian government or civilian government has betrayed the volk. Even when the civilian government does butt in it turns out the President and Senator Armstrong are super-soldiers themselves, fully part of the high level conspiracies that drive the MGS world.