I think the way a Thor/Hulk fight should be handled is Thor thinking Hulk is a danger, and trying to stop him. Only he doesn't use enough force, and only winds up making Hulk madder, to the point that Thor does something drastic like calling down lightning because a match of strength is not working. When one of the bolts breaks off a chunk of a building, causing it to fall towards some civilians, Hulk leaps into action, bracing the building before it collapses on top of them.
Thor, seeing this, realizes the error of his ways, and leaps in to help Hulk continue to brace the building. The two of them are just barely holding it back. There's one of the civilians (maybe Betty?) who is unconscious, and can't move out of the way. Hulk realizes this, gets super mad, and flings the building out of Thor's hands, toppling it back in the direction it came.
Once the danger is over, Thor drops Mjölnir, puts his hands up in a gesture of peace and says to Hulk, "Our fight is over, Hulk. You are indeed the strongest one there is. Not only in sheer power, but where it truly matters; the strength of a hero's heart. I was wrong for judging you by your appearance, and ask your forgiveness."
This scenario would serve several purposes. It shows that Hulk is the strongest there is. It also harkens back to the original lesson of humility that Thor learned in his banishment to Midgard. Finally, it shows that there is a thinking mind inside of Hulk, a hero who will defend the weak, and will only fight when he perceives a threat.