Let's set this straight. Goku is a warrior, he is the best, he goes with the dragon-thing and trains in heaven - whatever. We all know he is extremely powerful. He can bust planets easily, etc. etc.
But, is he made of atoms? Molecules? Elements? In terms of what he is as a product of the universe, is he any different from Walter Joseph Kovacs? The answer is no.
Because of that, Goku is destroyed. He dies. He loses.
Doctor Manhattan can't really be used in these fights because unless your a Toon or God, you are still made of atoms. Doctor Manhattan is a metaphor for the power that being like Superman, Thor and others seemingly achieve to be "Superman" among the "Supermen". He wins because he was designed to win.