And even if you go strictly by what's in the books, the detailed history of Delta Green is as a litany of horrors and screw-ups and corruption on the part of the org. The adventures and GM guidance talk constantly about agents going rogue, DG cells being ordered to wipe out other cells, and the toll all of it takes on the PCs, because of all the terrible stuff they have to tell themselves is necessary, like the deep state monsters they are. It's a horror game, and some of the best horror has no good guys, just various shades of bad, including people who are certain they're murdering other people for the right reason.