Sorry, but your counter example above is what is known as a straw man. As pointed out, general order 12 does not require Kirk to blow anyone out of space.
That's not what I'm talking about. I'm talking about taking the steps to prepare for active combat with one of your own ships. I'm really not trying to strawman anything; the above steps I describe are the real-world counterparts of things like "raising shields" or "red alert." What do you think it would take to get one American submarine to take those steps against another, no matter how peculiar the situation? Can you see why that would be a complicated decision? Even just psychologically?
Mainly I would expect Kirk to have been thinking that whatever the peculiarity of the situation, the possibility of another Starfleet ship firing on him was so remote as to be absurd. Which is in fact what I would expect the commander of a warship approaching a fellow warship to think, in most remotely psychologically realistic settings. So I suppose that explanation just seems like the most natural fit to me. I suppose we could count seconds from this or that indications that something is wrong and award Kirk a coresponding number of Alzheimer's Medals if you're really determined to, but I can't say I'm buying it.
Saito S wrote:
going to yellow alert (which - according to the dialog and visuals immediately following Kirk giving the yellow alert order - apparently includes "energizing defense fields" and charging phasers!) but not raising shields, seeing the Reliant raise HERS but still not raising the shields... sorry, but I really can't get past that.
That's your prerogative. Procedurally I kinda sort of see where you're coming from, it's just that the plot point is about psychology and that's where we seem to differ. (I have always admittedly found the "defense fields" thing a bit confusing -- shouldn't yellow alert automatically raise the shields? What's the difference between shields and "defense fields"?) On timing, the immediate preamble to Khan's attack is basically supposed to be extremely rapid, so I've really never found myself stopwatching Kirk's response time to the Reliant's actions once that begins.