Thinking about them and their fate, because no matter how many years it had been John still cared, sure he hated Dutch, but he still cared. Dutch was his father, his mentor, his saviour, the man who took the noose off his neck when he was twelve.
After Dutch's death, Agent Ross confronts John, saying "so in the end you didn't have the guts to shoot him," a reference to a conversation they had had earlier where Ross blames John for letting Dutch escape due to his remaining feelings for him: "Scared to shoot him? Too much to handle?" Where John replies: "when the opportunity presents itself I will put a bullet in him, don't you worry. I won't like myself for it, but I will do it;" admitting his distaste for what he must do.
Agent Ross's sidekick, Archer, also acknowledges the burden that Dutch's death took on John when he says "thank you mister Marston, I know this wasn't easy for you, but you made your country proud."
John knows what must be done so he does it, did it with Escuella, did it with Williamson and did it with Van Der Linde, but unlike with the first two, he shows an utter distaste. When he was in Mexico he went straight for the price, he had no troubles beating people to get information, no troubles shooting Williamson either. He did show some distaste when it came to Escuella, but he did it either way.
And then with Dutch, when it came to Dutch he several times tries to see if he can avoid it, trying to get his family from Agent Ross without killing Dutch, he even asked if Agent Ross couldn't just do it himself. He is way more avoidant of it, and the agents comments show it as well. If you chose to hand over Escuella alive, they joked around, but with Dutch they showed at least some form of compassion and understanding towards John.
And even though John said he would shoot Dutch, he didn't. He had Dutch at gunpoint several times but he didn’t shoot, even in the end he didn’t shoot, he stalled, he listened to Dutch talk, most likely knowing that it would be the last time. He knew that there would be no way of excusing Dutch's survival when he was wounded and trapped.
Dutch killed himself in the end, and I think that was a relief for John. Even though he would have pulled the trigger, he wanted to avoid Dutch's blood on his hand, he wanted to avoid snuffing out his father's life.
John did what he needed and would have done more, but he hated himself for it because no matter what Dutch had done, Dutch was still the man who saved twelve-year-old John, gave him a family and a home.
