Military discipline doesn't begin at big ordeals. Insubordination is nipped in the bud.
Na Ki was fine at this point.
It's when he commits to a deal with the Saki
and talks back that he crosses the line.
Then he silenced his general, for the second raising his hand as though Shin is subordinate
to him.
And when reprimanded by Shin, he offers a word of apology with his
back turned.
There were plenty of ways for this scene to go down without undermining Shin. As it went down, Shin had every right and reason to give Na Ki a stern talking-to and warning.
This could've been avoided with a "Trust me, captain" or whatever - something to acknowledge Shin trusting in Na Ki's intuition.