He should never have been down there endangering spock's life in the first place, and though morally it was the right thing, he did alter the natural development of the Nibiru native population, and broke Starfleet's #1 directive of not interference.
There is no further development period without the interference.
Yeah, Spock's preaching to Kirk about violating the prime directive made no sense, because Spock was doing the same thing by stopping the volcano!!
Like Pike said, they were there to OBSERVE.