In my version of the scene, all of what you're saying is accounted for. Notice I said that it's in his character to TRY something. Not that he'd succeed. To me, him not trying something breaks from the character they were creating.
I'm going to have to type this out and save it somewhere to trot it out when necessary, but here's "my version":
Everything same as the movie until Pa tells him to stop. He does at first, but then sees the tornado and just can't take it - he has to try. BUT to respect his dad not wanting the secret out, he runs over at non-Super speed. He easily frees Pa, but the tornado's coming too fast and they won't get away - so they jump into the cab of the truck. Clark has Pa lay on the seat with himself above, to try to use his body as a shield from debris. The tornado picks them up and you get shots of things striking the sides of the truck but Clark holding Pa close to protect him. The barrage dies down a bit, and Pa says: "I told you to stay. Why didn't you stay?" and Clark says: "I couldn't just do nothing and watch you die. You're my dad. (emotion building) I don't care what I said before, you're my dad!" (callback to "You are my son!", one of the best parts of MoS, imo). Then BAM!! Another hit and the back of the truck is crushed a bit by a tree, and looks like a close call. Clark, up to now mainly looking out of the truck, looks back to see if Pa's ok, and Pa starts to choke, blood coming out - Clark looks down to see that the tree that crushed the back also came up through the bottom of the cab - the one place Clark couldn't keep an eye on. I had some really (imo) good dialogue between them before Pa dies in Clark's arms, but I've forgotten it.
Now, I'm not paid to be a writer and I'm sure that someone who actually is would be able to clean that up and make it movie-ready. But the idea of that, at least, speaks more to the character than what we got. It's the modern equivalent of "all those powers and I couldn't save him" (even though that wasn't in my head when I thought of it) and it also has someone that dies because of/in spite of Clark's actions. He, of course, blames himself. And it would also do what the end of the Zod fight was said to be for - building his "rule". Blaming himself, he says that if he has any say in it, no one else will die by his actions.
But, anyway, that's my take on the scene.