Despite how "dated" the themes of DG are (which I have yet to be entirely convinced of), I think there is one essay that stands out: John Tynes intro, in which he denounces a cynical, apathetic populace that feels helpless to enact change and how it serves the purpose of the forces of the mythos.

Which leads me to the alternative I'd like to propose: the new Cult of Cthulhu. In the main Delta Green book it mentions that the classic Cult has disintegrated and now it is composed of individuals who have insinuated themselves in the power structure but are unaware of each other. Unaware, that is, until the stars come right and dread Cthulhu contacts them in their dreams.

Now, a legion of sleeper agents across all levels of society hear that obscene music of Ry'leh in their dreams, promising power in exchange for servitude to the Great Old Ones. Some of these dreamers, traditionally loners, artists and the emotionally sensitive, crack when faced with the cosmic horrors, charging into their schools or places of employment and enacting a personal apocalypse in a hail of gunfire. Those who are capable of accepting such things, the businessmen and other practical sorts, accept Faustian bargains and work towards social entropy. They are:

• Military strategists who push countries into senseless conflicts that destabilize the world stage, continuing to make matters worse by intentionally sabotaging occupational forces and stirring up resentment amongst the native population.

• Marketing agents who target children, instilling a sense of relentless consumerism at an early age, causing them not to consider the world outside of their immediate needs.

• Human traffickers who develop compounds on U.S. soil of indentured laborers, seperated from the larger society so that they can toil towards constructing some nameless and abhorrent monstrosity.

• Statistical analysts who, through narrow-casting, develop personalized political strategies of hate-mongering that further divide humanity, ensuring that we're too busy fighting each other to give any resistance when the stars come right.

• Account managers for international finance organizations that ensure a growing disparity between the first and third world through manipulative pratices, forcing privitization into economies that clearly are not ready for such steps.

... And the list goes on. These hidden cells of agents meet only in dreams, co-ordinating efforts under alien skies while they sleep, plotting humanity's end for the chance to survive the oncoming End. They do not dress in dark robes and cry out infernal names ecstatically in some ancient grove or swamp, but instead surround us, blending into the fabric of our everyday life. At least until they are well-hidden from prying eyes in exclusive country clubs or indulge in "corporate retreats".

Though the cultists might not necessarily know each other in the waking world, they would be able to tell, just from body language and other subtle cues, another member of the Cult. Certain Dreamers and Talents might also share this ability, making them crucial new recruits for Delta Green. Another alternative would be that they only are aware of certain other members of the cult, arranged in the "Xothian Dreamscape" by their master, to ensure compartmentalization.

In this scenario, the people above DG are the enemy (and the people within), just like what you proposed with the Shans. No one can be trusted, for who knows what vile pacts they have made in that life beyond the waking world? DG becomes a puppet used to eliminate potential threats to the Mythos, from apocalyptic cults to individual investigators for national security. Yithians, Elder Things, Mi-Go, Shoggoths, Flying Polyps: these are rival species that can be eliminated to make way for the time that Ghroth fall into orbit and Ry'leth emerges from beneath the waves. The only way to root out the traitors is dangerous and hallucinatory treks into nightmare worlds beyond human reason to confront them in dreams.