I don't think it was Lucas's intent for us to believe that Windu actually defeated Palpatine. After all, if Sidious could be killed at that time by Windu, then there wouldn't be much point to the prophecy that says that Anakin will kill him. I think Palpy was just faking it in order to gain Anakin's sympathy and trick him into coming over to the Dark Side (by striking Windu).