Additionally these guys knew that someone was blocking communications with the space station (and now they couldn't contact it al all) and then a ship shows up acting suspiciously! Come on, if the writers hadn't mentioned the existence of such a regulation they might have gotten away with it (ie. if no one had reminded Kirk!), but they oversold it so well there is just no excuse for Kirk's inaction.
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.)
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!")
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.
(EDIT: I think Ryan Britt
put it nicely:
Ryan Britt wrote:
One of the reasons we all [sic] love The Wrath of Khan so much is because it’s truly the first time James Kirk admits what an asshole he’s been his whole life. All of his arrogant mistakes come to bite him in the ass in this story; culminating in a scene in which Kirk sits around having a drink with his estranged son, lamenting how screwed up his life is. Wrath also finds Kirk saying “I did nothing!” in response to Sulu’s praise of everyone narrowly avoiding death. Here, we realize Kirk has adopted a fake-it-until-you-make-it philosophy his entire life, and once he is no longer a young man, this freaks him out big time.
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.