Togo was the main cause of the war and most of the crimes assosiated with it. The emporor had very little real power. Keeping him in after the war was a smart idea, because it kept the Japanese from rioting against us. Hirohito preached the western line after the war and it kept the Japanese placated.
First, it was Tojo that you are thinking of, as Admiral Togo (of Russo-Japanese War) was long dead.
Second, there were alot of governmental types, including the Emperor, supporting the war. His
role really was greater than initially thought.
Third, even with that, he was the leading force behind the surrender and threw his support behind the American occupation. Based on that, he should have stayed. He could have made it much rougher for the US, had he chosen to do so.