I think the most interesting thing I read here is that McCarthy, Ball, and Gutekunst report to Murphy.... That apparently puts them all on equal footing in the organization... and means the GM cannot directly hire or fire the other 2.
Gutekusnst is rookie in the "decider' business. You would not want to hand him the keys to the kingdom.
Once McCarthy established himself, Thompson would not have had the authority to just boot him on his own volition nor did McCarthy have sole authority to just boot Capers. NFL football clubs are small, top heavy organizations. These are critical decisions in the hands of a few people. You cannot expect the man at the top to just rubber stamp everything, or the #2 guy to just rubber stamp everything the #3 guy does, or expect the #3 guy to make his case about he needs and not have that opinion respected.
There are power struggles too, as evidenced in the winners and the departing or disappointed losers in this mess. In point of fact, I would not be surprised if McCarthy exercised influence to get Thompson booted upstairs just as Reid made his case to get Dorsey fired.
In a way this is better, if that's in fact how the org chart lays out. The power sharing and lines of authority to the top are clearer. Some years down the road, if Gutekunst can establish himself as a top GM, he'll earn more trust and authority.
And maybe Murphy has determined that he will be spending less time buying gas stations and building hotels and can apply himself more to the football operation.