Also the part about Johathan's death, I agree. I see what they were going for but the moments leading up to that crucial plot point are based on flimsy logic. Why couldn't Clark just get the dog? Even without powers he was faster than his dad. Clark is just standing their for much of the scene, his dad is delaying, why not go to him then. He hasn't been waved off, his death isn't unavoidable, and clark wouldn't have had to reveal anything. So why not run over there while there was still time? The distance didn't even seem that far. The scene just ignores basic logic.
The easy answer is "Clark is still a young man". Young people don't always know exactly what to do in a given situation,
Here's the thing about that scene. I don't think Jonathan's first line, "Get your mother to safety" is an accident. Jonathan wants Clark and Ma to get to safety. Like its his instinct to rescue the dog, it's just the man's instinct to avoid putting people in harm's way, even his (for all they know) indestructible son. And we don't actually know the level of Clark's indestructibility at that point, so it's arguable that Jonathan could well think the tornado might kill Clark, who, as we see, Jonathan considers pretty darn important.