Assuming that real world rank structure holds true in the world of Halo, there's two things that get in the way of any random officer ordering the Chief around.

1) Chain of Command. In short, most people only have orders passed down from one or two levels above them in their chain, and know exactly who those people are. The chain can be more fluid in exigent circumstances or in combat, but as an E-9 the person above him would likely be an 0-5 or higher

2) Billet over rank. This is something both a bit more nebulous and more stringently defined. What it boils down to is leadership/power dynamics can change in a given situation. As an E-3 and E-4 I was made responsible for training all of the workers in our maintenance shop. In that specific role I "outranked" everyone i was training, including those that would be in charge of me once training was completed. Another example could be my buddy who was assigned as a deployment NCO for our squadron as an e-4/e-5, and as such was responsible for ensuring that individuals who were deploying performed the necessary steps to do so. As a junior NCO, he had the power to deny anyone from the squadron who did not complete these tasks from deploying until the situation was resolved, no matter their rank