Those are all setup/framework scenes for action sequences later in the film. Kirk and Spock discussing the legality of the mission leads to Kirk deciding to capture Harrison, which ultimately results in a fight scene involving John Harrison and the whole rest of the film. Scotty and Keenser resigning sets up Scotty's discovery of the Vengeance, Scotty saving the Enterprise from the Vengeance, getting Kirk and Khan on the Vengeance, and everything else on the Vengeance. All these scenes are necessary for the plot, but they don't really form a cohesive theme besides "standing up for your principles at the wrong time gets people killed." And I'm pretty sure that's not what the writers were trying to say.
The message is that using long range weapons to execute suspected criminals without trial is wrong, which they convey just fine, IMO.
The scenes at the start of the film set up the action at the end just like in every other Star Trek movie ever, and a good portion of the episodes too. It's like saying the discussion of Genesis in Wrath of Khan was just a flimsy set up for a race against time sequence at the end.