Exactly.
And, Starfleet officers, supposedly trained professionals, would demonstrate professionalism to take their new CO's orders and follow them. That's their job in the service to the mission.
I think that everyone in the chain of command did just that. Here's a simplified version of what likely happened:
JELLICO to RIKER: Riker, I want to go to a 4-shift rotation.
RIKER to SHIFT LEADERS: The captain wants to go to 4 shifts.
SHIFT LEADERS to RIKER: That would cause serious problems. Do we do it anyway?
RIKER to SHIFT LEADERS: Let me talk to the captain.
RIKER to JELLICO: The shift leaders say it will cause serious problems.
JELLICO to RIKER: Don't care, do it anyway.
RIKER to SHIFT LEADERS: Do it anyway.
SHIFT LEADERS: Aye, sir.
At this point, no one has violated protocol. The captain has exercised his right, the first officer has done what first officers are supposed to do: pointed out a potential mistake, and the shift leaders have made the first officer aware of what's involved.
Since we cannot prove that the serious problems did or did not occur, we cannot debate the wisdom of Jellico's actions, or the competence of the shift leaders. But up until that point, all of the people involved had simply done what was expected of them.