It was too stupid to feel sorry for him.
I know of tragic tales of people who would jump into oceans and burning buildings to save their pets, so I can't fault Jonathan for doing that. But Clark offered to save the dog...He didn't even have to use his powers to do what Jonathan did. He got to the car in time and saved the dog, it was just the crush of it that dealt the killing strike.
And while it is admirable of a father to put his child above his own safety...It was just bizarre. Really bizarre. As The Question pointed out, there was no appropriate response from a man who was about to be sucked into a tornado, to his death.
The guy was either pretty suicidal, or just written in a pretty strange away. I think Costner's slight smile when he was about to die was because he knew he'd get his pay cheque after this last day of filming

Smallville had its faults, but John Schneider was a great Jonathan Kent...BECAUSE HE WAS WRITTEN AS A HUMAN BEING!
He would have doubts, but would never tell Clark not to do something if it wasn't the right thing.
He would be encouraging, while at the same time, fearful.
He would get angry, which caused him to lose his life.
Costner was pratically a robot, who was programmed to be a killjoy and give little to no emotion.
An admirable character, at certain times, but very oddly distant and unsure of everything, which rubbed off on Clark...
And his decisions were stupid and ones that didn't make him seem human in the slightest.