Huh. I have to say I don't think of institutional protagonists in that way. I mean, I'm somewhat sympathetic to players who want to be special agents who believe in what they're doing and all that, but the idea that there are two sides--our side and the wrong side--is patently ridiculous, and a game or narrative set up like that is weak and juvenile.
But I don't think that's intrinsic to the conceit of PCs as agents of an institutionally conservative status quo.
Take A Scanner Darkly for example. That's a story about a drug enforcement agent.
Or Solaris. Kris Kelvin, and all the other astronaut Solarists, are members of the governing institution.
And the description "agents of an institutionally conservative status quo routing out threats to American hegemony, who actually believe in what they do" also describes half the cast of The Wire.
The reason I use the drug war and the cold war as analogies is precisely because they are/were pointless bullshit. Just the espionage in the cold war ruined literally thousands of lives because of bad intell to begin with, never mind the ruination of third-world countries through proxy wars. Some people honestly thought they were fighting the good fight, and other people used it as an excuse to take over half the world, just like American drug laws are an excuse to put coloured people in jail. And hell, nobody really thinks they can win the war on drugs.
But I think maybe what you're reacting against is the idea of The Man? Or the heroic, unified front against the Eschaton, and having that portrayed through Man-from-U.N.C.L.E.-slick government agents?
I think the best way to approach it is through factions. If all of society were of one mind, there wouldn't be any problem--but that's not the case. Society is fractured, and everybody has different resources, has different concerns, is vulnerable to the eschaton in different ways, gets different benefits from the eschaton, AND have different alliances with each other.
It isn't about how well you fight the end. It's about how you work with or against the other factions, who goes down first, who becomes obsolete, how you make your peace with the end of everything. I mean, what do DEA agents do when suddenly heroin doesn't just get you high, it makes you telepathic? Etc.
Goddamn I write a lot.