Well, actually Order 66 took place in the middle of the war. Right after Order 66, Darth Vader wiped out the Separatist leaders, putting an end to the civil war.
I only point to one thing.
Palpatine could of never pulled off order 66 if the separatists had won. Remember Palpatine's plan was to weaken the jedi order and have them fighting a war that had most of their knights separated and alone completely dependent on the Grand army.
Separatists were merely a means to an end for Palpatine.