That went better than in the show. I guess Jordan being so sttuborn and defiant is taking a toll on Clark. Having a rebellious teen is bad enough, but having a super powered rebellious teen takes things to a whole new level. Jordan's behaviour has the potential to ruin the entire family's life. As he didn't make any progress with Jordan, he thought it would be easier helping Jon. Clark has a simpler way of seeing things. He grew up on the farm, the typical farm boy. And he expects the boys to see things like he did, react like he did, but they had a different upbring and things changed a lot. As when he invited the boys to spend time with him because "he loved spending time with his mother". Or when he didn't think anything wrong about Jon and his girlfriend being alone at home because he "didn't think about it when he was their age". Clark is ingenuous and innocent in a lot of ways and I guess it makes it harder to him to see that his sons aren't like him and that times have changed.
On the other hand, Clark may have realized that Jonathan is better than expected. He seems to be progressing, while Jordan is regressing. Good thing there's fanfic. It's going to be a long wait until the next season.
Andreia
