I heard this on the ROTS commentary I think. Lucas wanted it seem like after Anikan had killed Mace that he thought the Jedi wouldn't except his decision to sacrifice a Jedi to honor the laws and present Palpatine to the senate so he followed the Emperor's orders and destroyed the Jedi so that he wouldn't have to worry about them trying to kill him. This would explain why he didn't just cut the emperor down after he killed Mace, because he knew even though he did follow the law and save the emperor to be sentenced in court he had screwed up and had nowhere else to go. It is tragic when you think about it this way.