After decades of technobabble accreting, the Star Trek universe is surprisingly resilient to plot holes. Technobabble is the gaffa tape of scriptwriting, it can fix and hold anything together. Here is an "in-universe" explanation for the submerging:
In the event of the volcano erupting with a lot of ash, the dust of a Nibiru volcano and its electrostatic potential would cause ionic interference (1) with the confinement beam, leading to deadly pattern degradation in the transporter signal. Communication with crew on the ground would likewise be hampered.
Note that in the movie, Spock is at some point in the volcano but unable to be beamed out, due to interference (2). This shows that we are dealing with a particulary bad volcano transporter-wise. Wouldn't want the crew on the surface and the Enterprise in space if the volcano erupts and the material causing the interference spreads to the atmosphere. (We can here assume that Nibiru already suffers from Trinimbic interference (3) .)
When quizzed, screenwriter and producer Roberto Orci came up with a similar explanation on the spot (2), only adding that it's magnetic interference, not Trinimbic. (Dumbing it down for the journalist no doubt ;-) As an extra precaution by the producers, Scotty is questioning Kirk's decision on submerging