I'm thinking of this as something that cross over boundaries, not purely an Inquisition Faction, but more of a cult with strong Inquisition Patronage - something like the Templar Orders before Philip's purge, where you had the Monks at the top, but also they provided support and protection to Lay Orders of masons, carpenters and the like who built their castles, and that spread into guilds of various kinds.
The reason it isn't considered heretical by the powers-that-be is that 1) the powers-that-be are often those who are most open to this idea, as they can see how everything really is wearing out and crumbling and 2) it doesn't say that the Imperium is worthless and will be defeated, but that EVERYTHING is going to die. The fact that they build massive shrines (to leave their mark on the Galaxy) and preach bravery in the face of defeat also helps.
Eco is very good at capturing how people can simultaneously know something is a lie, but believe, even as they craft the lie themselves - it is a lie of facts, not of spirit, etc. This would be pertinent to the post-Heresy High Lords and Primarchs, how they allowed the Imperial Truth to be hidden and suppressed, and lied about what the Emperor really said, because it is what he would have said, or should have said, to protect Mankind... And so, so quickly, it becomes what he did say.