The problem is that as a kid he is both wanting to 'just continue to be your son'/a normal kid AND save a bunch of people/use his powers. It was Jonathon Kent that wanted him to keep his abilities a secret as a kid, not Clark. He just wavers back and forth through the movie and so there is no identifying moment of change.
The problem with Clark's motivation lies in big part with the characters of Jor-El and Jonathan Kent. Clark was often depicted as blank canvas filled with the moral code and ethics of is human side and the training of his Kryptonian side. I remember that the Donner version had Clark stay a couple of years in his fortress of solitude to train.
This could have been made into a great point in MoS.
Jor-El who at Clark's birth already said to Lara's "He'll be an outcast. They will kill him." "How? He'll be a god to them."
Jor-El should have been the force behind Clark's will to train his abilities and use them. He should have told him that he is something better than them. While Jonathan should be the origin of his moral strenght and honor. Instead Jor-El is the guiding light morally as well as the one who makes him unleash his potential.
Jonathan Kent appears funny enough to be the representation of xenophobia (just like Lara-El) and quite morally ambigious, for whatever reasons:
- "No matter what kind of man you'll become Clark,
good or bad, you'll change the world."
- "What should I have done... let them all die?" "
Maybe"
- " you will have to make a choice, a choice if whether you will stand proud infront of the human race
or not.
- "I wanted to hit that kid" "I know you did,
part me of me even wanted you to, but then what?"
Goyer and Snyder decided against the traditional roles of Jonathan as the morals and Jor-El as the strength of Superman and made
choice a huge deal in the movie.
Free birth and the choice to be whatever one wanted to be. "What if a child dreamed of becoming something other than what society has intend for him. What if a child aspired to something greater?"
Jonathan giving Clark all these moral choices to decide for himself.
And to what does that lead us? Clark being morally unfocussed, even walking into a church for moral and spiritual aid.
This of course was the biggist "in your face" offender along the ride of Space-Jesus references (him being 33, the Jesus-shot side to side in the church, the Jesus-shot while getting out of Zod ships reminiscent of the Superman Returns Jesus-shot, him even asking Jonathan "Why did god make me that way?", Clarks actions being described as "divine interventions" by Pete Ross' mom, up to the point were Faora describes hereself as the evolutionary superior because of her lack of morals which could be a feel good point to Creationists everywhere... well fuck this shit).
These are the clearest offenders in terms of characterization which then lead to neck-snapping (instead of putting hands in front of eyes, flying away with Zod in a choke-hold) and Clark deciding against genocide against the human race, but blowing up the entire genesis ship and whiping out what was left of Krypton with the reason:
"Krypton had it's chance"
That's why anyone arguing that Supes killing the last Kryptonian was such a hard choice for him... now he is alone, and whatever: Nope! He basically whiped out his own race before he killed Zod.
The movie is filled with weird inconsistant choices like that and I'm not even going to start nitpicking the whole "atmosphere change, when are Kryptonians super-powered and when not, and how strong are they?" thing.