Space Marine Sovereignty

[DarkKnight]

And especially as the Inquisition have plenty of other Chapters such as the Crimson Fists (or Grey Knights for Emperors sake!) who are happy to fight alongside the Inquistion.

and Sisters of Battle, their own private armies, and IG or PDF they want. etc etc.

Space Marines do what is best for Space Marines. They have a big interest in seeing the Imperium servive since they life within the Imperium and they get there recruits from us little humans. Without the Imperium the Space Marines do not exist so if they want to survive than they will usually be helpful if it suits there interests. When Space Marines help a Warmaster than they more or less earn a favor from that Warmaster. All of this leaves the Inquisition from questioning there worth.

[Intrepid]

No, I think Space Marines are autonomous, not sovereign...big difference. Sovereign means they can do anything they please, which isn't the case as they still answer to both the Inquisition and High Lords. (Space Marines cannot refuse Inquisitors without a good reason and the High Lords speak with the Emperor's authority.) Autonomous means they're given general orders but may decide how best to get the job done. If Marines could do anything they wanted then Chapters that turn on the Imperium without joining Chaos (like the Soul Drinkers or Celestial Lions) could not be Excomminucated, Chapters could not be ordered on penitent crusades and so on. Marines do have masters, they're just few in number and don't have time to micromanage.