To me it makes a lot of sense for the Inquisitor to be the center of a web of intrigue radiating out from him, a hierarchy of his agents with him at the top, radiating out into his personal friends and assistants down the ranks. Just like the relationship of a general of an army to the officers, NCOs, and enlisted underneath him - and then reaching out father to merely people who sell him information but know not where it goes.
Regarding the deviation from original material: obviously GW is ok with it or they would have tried to pull the plug on the license. The brand isn't static, after all. You can still have a rivalry and I don't even have a problem with the real rivals being NPCs. To me the greatest disservice DH did to the source material was Ascension making that high-level play literally unplayable due to the awful rules at that level.