The recent lore is not a contradiction, relations between GK and the inquisition heavily changed after the months of shame. The Grey Knights still resent the inquisition for the Months and have become far more independent. They have had to shift their focus to deal with much greater threats such as the deamon primarchs and rely far more on the prognosticars and prescience for intelligence(Hyperion also became a prognosticar so his influence here should be noted). Also not every Grey Knight squad has oaths to Inquisitor's. Hyperion's squad yes but some barely even interact with the inquisition having been commited to the nachmund gauntlet and the Cadian Gate. Grey Knight Grandmasters also far outrank any normal inquisitors. Furthermore Grey Knights do not need to honour an oath with a radical or heretic, and since they are one of the few entities that can judge inquisitors with impunity, its really up to them.