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. ... .
As Saito S
pointed out there is no analogue to raising shieds in present warships (I thought about mentioning that, but was just too damned lazy!
), so your example breaks down at that point. To make that clearer: What commander would fail to termporility double their ship's armour in a suspicious situation if they could do so at the flick of a switch? None I'm guessing. There is no Rubicon being crossed as there would be with preparing for offensive action in current day terms. So I can't see the problem. But even it there is any residual psychological resistance, that presumably is precisely why GO 12 exists.
To be fair I can't remember if that scene stood out like finding Spock on the ice planet in ST09, or not. Certainly not as badly I'm guessing, but I still think it is the worst such moment in TWOK, and I tend to over look a lot of that stuff unless someone draws my attention to it.