I view the we're-taking-this-ship-not-you-scene as being mostly a non-issue for the Navy men; they're requisitioning civilian ships to rescue hundreds of thousands of men, and as long as those ships end up at Dunkirk and pick up men, they probably don't care who's piloting the damn thing. In real life, the Navy flat out emptied whole harbors of ships even if the owners weren't aware of what was happening. If anything, that crew that silently watches our protagonists sail away probably just shrugged and presumed they'd be manning a boat regardless.
It's also important to note that The Sea's protagonists are *not* part of the military. They're not subordinate officers or enlisted men, so there's really no "insubordination" at work here. They could theoretically be placed under arrest, but why? What would you gain from stopping men who crewed a rescue ship and successfully brought back a boatload of soldiers? As civilian volunteers? They're not getting any glory or money, they're not part of the chain of command, they're just some civilians who pulled men out of fiery water and brought them home.
Kirk and your regular military archetype characters are part of the military, and thus subject to the "reckless maverick" characterization. These guys aren't.
Saw this a second time last night. It was better on the Imax, but is still a damn good movie. Nolan's mastered his technique and remains an incredible storyteller.