I have honestly never questioned what it takes to be classified as a xenos threat by the Imperium, and what makes you stock. My guess (much like a simplified form of Gobmaw's theory) is that if it can hold a rock (like the early Tau), kill it. Otherwise it counts as food/pet/wild life. It's not just that the Dark Angels are team-killers as above, but the Fallen are a secretive group themselves (probably because of their team killing family). They don't broadcast themselves as Dark Angel heretics from the Horus Heresy. Even if they did, the only people who get really upset about it are the Dark Angels. There have been so many renegade chapters of all gene-seed variety that seeing a traitor Dark Angel isn't some revelation for the Inquisition. Not to mention the Fallen fear the Inner Circle more than the Inquisition, so if captured probably lie and say they belong to a later founding chapter. The Inquisition aren't actively looking for the Fallen among the heretics, the Dark Angels are.