I looks like the Federation totally miscalculated the Klingon time table and size of the fleet sent to Organia. Eight ships showed up days or weeks earlier than Federation plans. Kirk's mission was doomed before it began. Since Sulu returned with an equal or better fleet within a day or two, the idea that ships would be ready to take up defense of the planet would be the best scenario. Kirk's probable mission was to evaluate the population/government of Organia, and make contact with them to get their permission. I surmise that friendly planetary support would be needed for a fleet in orbit. Maybe there is some legal standing to be under the protection of the Federation (invokes treaty commitments from other alliances besides just the Federation). The surprise attack of the Klingons in large force trumped his plans. I take Kirk's comment, " If you had listened to me..." was more a statement of his frustration to himself than a real complaint to the Organians.