Well that's just the thing, the brand of "conscience" that he offers has to be outright rejected in order to become Superman, rather than being the motivating factor for superman. He has to go against Kent's wishes to do anything heroic. Again, a deterrent rather than a motivation.
Jon never told him to not save people, he told him to keep his godly self a secret until he knew why he was here(this realization came in the form of Jor'EL exposition and the costume and then with Zod). Until that time Jon never said don't save people he said don't announce yourself. Save all the people you want if you can practice ultimate discretion, this led to the mysterious ghost savior(as seen in much of the cannon blue blur/birthright). The only deterrent jon offered was that clark needed to keep his secret. If that's too much of a deterrent for you than this might not be the genre for you.
You see, it could be argued that superman and superheros in particular could save more lives and be more heroic if they didn't bother with all the secret id crap changing in phone booths and all that stuff(however they know better). There is sometimes a greater good in practicing discretion.
Also, while that scene with the bully is great, it does not at all play out in the rest of the movie. What is Zod if not a bully? And if the bully scene isn't relevant to anything else, what is the point of specifically flashing back to that moment?
Here's my problem with this criticism, it's making the wrong and quite frankly most basic correlation to Zod. It's when people do this and then criticize a story for lacking complexity that I feel disheartened.
Jon's advice about bullies was to inform his godly son about how to deal with bullies, something Jon knows his son is bound to encounter in this world. Our world. Jons gives his son advice based on the world and experience he himself has lived in. Jon didn't advice his son on how to deal with a doomsday creature, nor did him advice him about a backwards superman. He told him about how to quell his anger and deal with idiots like the human boys that were clearly below him in both power and integrity. If you want to see how this advice informed who superman becomes look no further than the bar scene in which we see Clark exercise his fathers advice prudently...on that "bully".
Watching the Spiderman films, we see an example of how some hero's misuse their powers on mere mortal bullies. Watching the donnerverse we see even more of that. In MOS, Jon influenced his immortal son with a mortal heart on how to deal with mortals below him. There's your advisory purpose filled. If you want to see Jon advise his son on how to deal with super villains, perhaps we should see a jon that knows of their existence. Or perhaps a film that is more simplified in which Jon just says bullies are bad in all their forms. Punch them.
So what Pa Kent's mixed messages amount to are either advice that is completely counter to becoming Superman or, if it is sound advice, is completely thrown under the rug.
I would argue that Kent's message informs who Superman is to become. A simple hero in a complex world.
A world in which the ultimate good and the immediate good aren't one in the same. One in which people aren't simply celebrated for having costumes and being able fly, one in which being a hero might just come at a cost to one's self.