Finally came back to this answer after a while. I found the story I was looking for:
In the short pre-Crisis tale Martha's Story , by Samuel Hawkins, a dying Martha Kent is recalling various aspects of raising baby Clark. Several instances are referenced where his inhuman powers were showcased as him being a "handful", mostly due to his young age and resulting lack of control. The full short story can be read here:
Excerpts from it give detail....
"It would be nice to think that once we snatched Clark up out of that rocket, that everything was okay for him. But it wasn’t. Those first few months were rough. Being under our sun was quickly developing his powers, and adjusting to them was harder than you’d think. Suddenly, everything about him worked so much better that it was all happening too fast for him. We had to work very hard with him to slow him down. To teach him how to live at a human pace....
It continues [emphasis mine]...
"To say that Clark was a handful when he was a toddler would be an understatement. Most kids are, after all, but a child who hardly ever gets tired is something else all together. No naps for that boy. He was always on the go, hanging off the ceiling, or running around so fast that the wind he kicked up would pull things off the walls. Why, I didn’t think I would ever teach him to not use his super-speed in the house .....
I'm highlighting the next part to show how even from an early age, Clark's mental control was implied.
Of course, we would be kidding ourselves to believe that we could have ever made Clark do anything he didn’t want to do. No, him obeying us, allowing us to discipline him and parent him, always required his cooperation. He figured out that little fact pretty quickly, but he never took advantage of it. I guess his consent, unspoken though it was, was due to the good parenting Lara and Jor-El did in the time that they had him, and the fact that he was so smart, he somehow understood that he needed parents to teach him how to behave.
Of specific interest here is this part:
...He shot out of my lap and ran outside, and the next thing I knew, he had punched a hole in the little concrete pump house we used to have out back. Then he punched it again, and I could see that the whole thing was about to tumble down. I imagine it wasn’t the brightest thing I’ve ever done, but I ran up behind him, forgetting what someone as strong as him could do to me...I grabbed his arm before he could swing again, and he jerked it away from me so fast that I went down onto the ground. He didn’t mean to do it, but he flung me down like I was a rag doll.
I looked up, and he was just standing there, this terribly angry look on his face, looking for all the world like he wanted to keep on hitting something. And with me being the closest thing at the time, I wasn’t all together sure that something wouldn’t be me....But then he saw me lying there, and saw what he had done. I’m pretty sure that was the first time he realized just what he could do to other people. And he just melted. He fell down on the ground beside me and sobbed and sobbed. "Not hurt Mommy," he kept saying. "Not hurt Mommy."
The moment before, I’ll admit, I’d been afraid of him. After that, I never was again. He knew what he could do, but he was smart enough, and good enough, to never do it."
So it seems that, from Martha Kent's own words, the Kents basically had Clark's respectful and obedient "cooperation" in raising him. Being that he was so much stronger and basically unstoppable, they couldn't "force him" to behave like regular parents. So it would appear they more "lead by example" and appealed to his unusually high intellect and "better nature" of him basically being a good kid.
This kind of falls in line with the 2000s Smallville interpretation of Clark as a teenager, as well; although that version had plentiful amounts of "meteor rocks" they could use to make Clark sick and weak, if need be, the Jonathan and Martha Kent of that universe were noble, hard working, stubborn "salt of the earth" people who were often kinda strict, rule-focused and over protective of their son. Still, even with those strong mid-western values, that show in particular showed them to be a core aspect of Clark's foundational character, based on their closeness to him and the values they taught:
so it would seem, regardless of the version, Clark was raised with a combination of careful structure and TLC by the Kents, with a lot of compassion which helped shaped how he saw the world. as such, there was little need for them to "discipline" him like other, normal children.