Nothing against the shot, but there was no valid reason, and that makes it bad writing.
Even if you only connect cool images with a script, you can give every cool shot a valid reason.
Put the shot in the last act, for example. The Enterprise is chased by the Vengeance, and there seems to be no escape. So Kirk, being the unconventionally out of the box bad ass he is, comes up with the idea of hiding the ship for repairs where Marcus/Khan will never think about looking for them: on a planet, under water.
When the repairs are done, and Vengeance is in range, rise out of the waters for a surprise attack.
Not only is there a reason now, it also makes the scene important.
That works at least for me because the whole subplot in the first act was pointless imo. Kirk breaks the Prime Directive, gets demoted and five minutes of screentime later gets promoted again. You can cut the whole sequence out without changing a thing about the story.
Similar annoyance that would have been extremely easy to get rid of was the way they incorporated old Spock into the Trek 2009 script. He was just sitting there in a cave waiting for coincidence to happen. That could have been easily rewritten to remove all the contrivances while keeping the same pacing.