Yeah, but he consulted Charlie Casserly, who was a decidedly mixed bag as GM.
There needs to be separation between football and business (outside of the cap and cash budget for players) and between upper management and football. Murphy has bent two walls Harlan put up for a reason. One was the CEO's direct involvement in football decisions (Parins' model). The other is the Exec Committee interfering in football operations. Murphy can choose to avoid the former by being wise and restrained. But the EC can force him to intervene as in the latter because he is their employee and he has breached the wall already for the coach, so it will be harder to refuse.
If they win, no one will care. That is true if they governed by Ouija board. But if they have tough times, this structure invites more silos, not less, and internecine warfare between departments that instead of being ignored by Thompson, will be brought to Murphy's door to fix. Any business student can tell you the silo problem cannot be solved by putting management in a room once a week.
I suspect that the communication issues largely revolved around the "people are not taking me seriously" or "people are not listening to me" variety and centered around Ted.
1. He won't take cues from Pro Personnel about FA
2. He gives the coaches players other than those they prefer
3. Coaches take the players and play them out of position
All of this is normal in any football organization. No one is ever completely happy. Thompson kept a lid on it internally and publicly. Murphy has now given it a weekly meeting. Crediting Rand, Murphy did address this directly and took the responsibility himself, so he has not abandoned the staff to consensus building alone.