How often did Stoick lie awake late at night and regret the decisions he had made? Stoick was the leader of an army in a war, and though his people are great fighters on their, they still take orders from him. While he may be an excellent leader, no warrior is infallible. They make mistakes. And those mistakes are the kind that get people Stoick cares about injured or even killed. Stoick knows this, but likely he still wishes he could have done something different so that he would not have had to bury a friend or break the news to yet another family that someone they love is dead.
And after the war was over - what of Stoick then? Now that he knew the truth about dragons, how much did it weigh on him that he did not listen to Valka sooner, that he lost her and caused fifteen years worth of others losing their loved ones? The war could have been that much shorter if only he had listened and tried to find another solution. The dragons, too. Did it pain Stoick to look at the dragons and think “I killed so many of you and you were innocent the entire time” and feel sick inside? That he, personally, caused so many deaths to the dragons even though he was trying to protect his own people?
War is not a pretty thing.