Actually the Sanghelli average is 7 foot, 4 inches to 8 foot, 5 inches. The average for a Brute is an astounding 8 foot, 6 inches to 9 foot, 2 inches. Master Chief is an exact 7 foot, 2inches, in armor, and 6 foot, 10 inches out of it.
That means that, in armor, Master Chief is 2 inches below the average height of an Elite. Spartan IIs were made bigger than most other Spartan classes. Let's not forget that comparing his height towering over a Spartan IV just is not fair. Spartan IVs are tall, but no where near as tell as Spartan II's. Chief already had greater physical traits, such as height, when Halsey first examined him at age 6.
If Master Chief doesn't seem like he is towering over Elites and Brutes, then that's probably right.