MoS Superman isn't a 'sociopath', but Snyder's obsession with objectivism really showed as the thematic mold around Clark's character and moral compass. You can't have your spandex hero seriously debate whether or not it's okay to let kids die and then wonder afterwards why no one gave a **** when he died in the following sequel. And the faux-solemnness and wooden nature of Cavill's performance was no doubt deliberate on Snyder's part; if he wants those objectivist themes respected, then Cavill can't go around with his fists and his hips declaring peace and justice for all. No, he has to be conflicted 100% of the time, no room for optimism or fun or whatever.
And the clunky execution that falls short under logical scrutiny is just classic Snyder tomfoolery; if Clark can move at supersonic speeds casually, no one at the scene of the tornado would have noticed him saving his father - especially not with the chaos of the storm in their midst and all of them likely under duress. And the kids who 'saw' what Clark did? Why did the adults even entertain them considering most of them were on the verge of drowning before they were saved?
To your second paragraph first: I agree that the Pa Kent tornado scene was clunky. But it wasn't the concept as much as the execution. The could have found a better way of arriving at the same point.
To the first: At what point does Clark wonder whether it was ok to let the school kids die? If anything, he risks his identity to save them, something he does multiple times during the movie, either risking his identity or risking his life because he
knows that saving lives is more important. How does this make it harder to support him or feel for him? The fact that Lois was able to backtrack Clark's identity from the Arctic all the way to his doorstep in tiny, middle-of-nowhere Smallville simply due to the presence he has left behind through the years also illustrates what kind of person Clark is, one who saves people.
I think your issue is more with Jonathan Kent, not Clark. However, I think many people are interpreting Jonathan's "maybe" as him essentially saying to Clark it's ok to let the kids die. But watch that scene, listen to the music playing, watch how Costner plays that scene. It's pretty clear that he is struggling with what to do. We are not used to this out of Jonathan Kent, this uncertainty in how he should raise Clark. We expect that he has all the answers. But what Snyder was trying to do was show us a special being having to come to terms with what and who he is, and how his parents would handle that is part of this. What if Superman comics never existed? What if we didn't have them in our minds to compare this to? Because this version of Jonathan Kent doesn't have that to go by. He is making it up as he goes along because there is no instruction manual on how to raise an alien boy with incredible powers.
But Jonathan did not genuinely want Clark to let those kids die. We know this because Clark is a hero. He saves those kids on the bus. He saves the kid who was bullying him just seconds before. He tries to protect the waitress. He saves the people on the oil rig despite knowing they would see his face. He puts his life on the line by giving himself over the government, by fighting trained Kryptonians, by taking down the world engine despite the fact it's weakening him, by fighting Zod, and any other acts of heroism that Lois found out about in trying to find him. Where did he learn this from? We also know that on two separate occasions, including the one directly after the "maybe" line where Jonathan is showing Clark his spaceship and speaks to Clark about the potential of standing proudly in front of the human race, and then later, after Clark is bullied, he again tells Clark he is gonna change the world. In BvS, Clark tells Lois that Superman (the idea) was a dream of his father's.
I don't see how any of that shows us a Jonathan Kent who did a poor job raising Clark. I just see a guy doing the best he can, a guy who is also scared that if his son is found out, he will be taken away and treated as a lab rat and will never have his life on his terms ever again, and this is very human.