That's easy. The Smurfs and their Custodes allies can just kill anyone who doesn't go full hero in a civil war. Hell, just add some ''tolerant'' and ''diverse'' factions hiding within the Imperium to come out of the woodwork and help the Smurfs and Custodes kill or restrain any of these crazy idiots. Or, factions like the Dark Angels might find an ''epiphany'' and turn good, accepting women and trannies into their ranks. Or Belisarius Cawl, genius that he is, might help the Blood Angels find a cure for their Red Thirst or Black Rage. Or Guilliman can tell the Black Templars to go crusade on some world near Chaos space, and they all get killed or whittled down to the point where they can no longer pose a threat to a progressive, tolerant Imperium because their numbers got chopped down to 1 percent of what they used to be.
Again, all it takes is a penstroke. Back in 2000, you would never believe that randos from Mars can be made to join Space Marine Legions that didn't train them, but the Primaris showed otherwise. If we were operating with old Imperium rules from 1999, the Primaris would just get shot or thrown out. Hell, we're all talking here because an order that once accepted only the SONS of Terran Nobility suddenly had chicks in their ranks who aren't Silent Sisters. If they can fuck with the lore by doing that, they can obviously do more.