If Dooku could be not only a rogue Jedi (and not a Sith) but also not the 'in your face' senior partner of the Confederacy it could be done.
His footage could be moved from Geonosis to the Jedi Temple.
His fight with Anakin from Episode 2 could be merged into his fight in Episode 3 making for one battle or the foe in the earlier match could be Grievous.
His final fight could replace Mace.
He turns after defending Palpatine who uses Dooku as proof of a Jedi conspiracy.
If Dooku was duped into backing the wrong horse Palpatine could build a conspiracy around him still acting as a current member of the Council.
It would take some nifty voice editing.
Shame Qui-Gon and Dooku can't be made to merge though.
Stupid Lucas.