Order 66 is one of a group of contingency orders, it's hidden within official protocols, and with Palpatine's death there's a few candidates for who would have the power to implement it, all of whom are in the tank for Palpatine and the Empire. Like if the Jedi kill Palpatine, the key difference is that Tarkin or Mas Amedda gives the Order instead, and while maybe Mace and Anakin can save some of the Jedi in the temple all of the Jedi out in the galaxy who died in Order 66 are still dying.