A key element in the opening part of ST:ID is that everybody is frantically improvising.
Scotty may have his objections to hiding underwater, but this odd predicament is extremely recent news to him. He's still bitching and moaning about it, after all, and being all jumpy about the sight of fish. Meanwhile, McCoy and Kirk are on a time-critical mission where neither knows what the other one is planning to achieve, while Sulu and Uhura are operating hardware unsuited for the task at hand and Spock is busy committing suicide preparing in situ a device Ensign X'Pendable or NCO Nowan could have deployed if pre-prepared. Clearly, forethought is something the heroes have had no time for here.
So it is up to the audience to speculate upon the reason for hurry, and the steps that preceded or precipitated the hurry instead of being mere responses to it. To wit, did Kirk go underwater because of the hurry? Or did going underwater allow him to realize there was a hurry? Or did going underwater appear sensible to him before he realized he was in a hurry?
If Kirk's mission when entering orbit were to stop the volcano from blowing up, he no doubt would do it from orbit. But the hurry suggests this is not a mission, but rather a reaction to a major shift in original mission parameters. Meaning two distinct interpretations appear:
1) Kirk planned on setting up shop underwater in order to conduct an innocent longterm survey, perhaps not (just) of the natives but of some phenomenon best studied underwater. A submerged base would cater for the regular deploying of underwater craft better than the flying of all those craft down from orbit, say. An aquashuttle like the one from TAS would need to spend unacceptable time puttering from a distant, beyond-the-horizon clandestine insertion point to the operations area if launching from orbit. The emergence of the crisis meant the mothership herself had to emerge from water at a non-clandestine spot, though.
2) Kirk planned on conducting an ordinary orbital survey, but the crisis he discovered prompted him to take his ship underwater instead. For what reason, we can further speculate... He was always planning on violating the stricter interpretation of the Prime Directive anyway, in getting the natives to leave their town. For all we know, his Plan B or C all along was to shepherd the natives into the Enterprise if everything else failed, an action better conducted physically than via transporter, considering the numbers supposedly involved.
Whether we pick 1 or 2, it's up to us to worry about the details. They don't alter the actual plot one iota, as Kirk's defying of common sense and the PD is a fixture no matter what, well established in dialogue.
Timo Saloniemi