I wouldn't say so. Most importantly, the regulation quoted at Kirk is in-context most likely written to apply to non-Starfleet vessels. It would be very weird for Starfleet to have protocols in place requiring its own vessels to be preparing to go to guns on each other in any remotely suspect circumstance, as that would be a recipe for unnecessary disasters. (I hate resorting to speculation but this one seems reasonably sound to me.)
Well the regulation is not about opening fire on other vessels, merely to show caution where warranted. And the circumstances at that point scream a need for caution for the numerous reasons already given. Moreover, general order 12 states: "On the approach of any
vessel where communications have not been established …".
Given this, acting as though it is totally inexcusable for him to be wary of applying this regulation -- and wary of leaping to conclusions about the situation in general, and generally unwilling to assume that a fellow Starfleet vessel would fire on him -- just doesn't make sense. Especially since we have seen Starfleet officers go the extra parsec to give each other the benefit of the doubt on the show previously, at considerable risk to their own vessels. That's why the Enterprise wasn't blown up during the disastrous wargame exercise depicted in... "The Ultimate Computer"? The one with Dyson and the M-5. (If anything is suspect in the scene it's that Khan, whose inexperience is later a plot point, seems to know and exploit this element of Starfleet psychology more surely than he should. "We are one big happy Fleet!")
If I was to speculate, I would guess that there were some hard won lessons that necessitated "non-Starfleet
vessels" to be changed to "any
vessel" in general order 12.
I don’t recall the exact circumstances of "The Ultimate Computer" but, as pointed out by Saito S,
in this case there is simply no down-side to raising shields and every reason to do so given what is at risk. The example you give probably had a down-side/up-side balance to be considered (they usually do). But I agree with you about Khan’s conclusion being a question mark. Perhaps that’s a "standard" navy attitude in all services, or maybe he discovered Starfleet attitudes while reading on the Enterprise 15 years ago?
Combine that with the fact that the "coil emissions" and shield-raising business all happens in very rapid sequence... again it's obviously a bad mistake, but it isn't rising to the level of inexplicability Saito seems to be alleging. At least not for me. It really does seem to me to be a species of overconfidence; not in the sense that he's not puzzled by the situation, he is, but in that he's so used to ignoring regulations in favour of his own instincts that he doesn't even realize his instincts might not be as sharp as they were.
There was enough time for Kirk to be warned, for Spock to over rule the warning and for Kirk to ignore it. Even with a mutated species of overconfidence, given the no down-side thing, yes its still almost inexplicable to me. I mean if you have seen those air crash docos there is often a "reason" for the weird things some people do but you still shake you head at them.
Basically a useful test is to translate a situation like this into a real-world analogue, especially in a Trek movie that's clearly based on a war movie setting. What level of suspiciousness would it take to get the skipper of an American nuclear submarine to conclude that one of his own vessels is a threat, plot a firing solution on it and flood his tubes in preparation to shoot it? Even in a situation of several suspicious-looking coincidences, at what point would he go to red alert and go to battle stations against one of his own vessels? I don't care what the circumstances are, crossing that Rubicon would be far from a simple decision. And in essence TWOK plays a parallel version of those kinds of uncertainties, and for once has Kirk choose wrong.
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. It is defensive precaution only. That being the case, I think Kirk would be incompetent to choose wrongly. I mean there is no anguished decision making needed here. It should have been the first thing he did, certainly after being reminded of the "general order". The requirements of the plot are one thing, but they made Kirk and Spock look worse than they had to in their effort to show Kirk as fallible, in my view.
BTW, I wouldn’t characterise Kirk as an ass-hole his whole life just because he doesn’t believe in the no-win scenario. A little unrealistic maybe?
Edit: I have been assuming general order 12 requires the raising of shields. But Memory Alpha suggests: "it is implied that the ship is supposed to go to yellow alert when faced with a non-communicative ship."
Hmmm ... yellow alert didn't seem to do much good!