I would say that the Wolves and Black Templar are two chapters that work closely with the head of Terra. In fact it was mentioned in the Heresy that the Wolves only answered to Malcador and the Emperor. Would not be surprised for the Wolves and Black Templar being supported and protected by Inquisition and High Lords of Terra.
I can see that most of the inquisition would see the benefits to keeping the wolves on their good side.
The ones against them would be the radical faction.
Conversely, I see both of these chapters as ones that don't work closely with the Council of Terra or the other higher authorities. In a classic 30k/40k turnaround, they have both gone from being perhaps the closest and most undoubtedly loyal of Legions, to being highly suspect. In the Crusade and Heresy days, the Wolves were Malcadors Legion it would seem, through him they and Russ it would seem, were almost beyond reproach of the others, for example, when Dorn ordered all Legions that were not his own off of Terra at the onset of the Heresy, he could not send the Wolves away as they answered to Malcador and not him. The Fists, were also obviously as close to Terra as any Legion could be, and worked closer than any other.
Switch to 40k, the Wolves don't answer to anybody seemingly, they utterly disregard the codex, they do as they choose and they don't give a damn about what the High Lords of the Inquisition want, the First War for Armageddon showcases this perfectly. It would almost seem that in Malcadors death and the Emperors ascension to the Golden Throne, the Wolves were unshackled as it were, and did not see fit to serve the bureaucrats that took over. The Templars are another, where as when they were part of the Imperial Fists, they were the praetorians of Terra, they now range away as far as they choose, with a chapter number that no body truly knows, and once again don't exactly follow the codex.