It's been made pretty clear that he NEVER actually fought as Sidious with the separatist army, and never fought PERIOD as chancellor until he was discovered at the end of episode 3.
And had he fought, he had to stay in whichever character he was posing as just to maintain the lie. So Sidious would NEVER fight for/with the Republic. Just to drive the point home as to how different they were, Ian McDiarmid was never told Sidious, and Palpatine were the same person during filming of episode 1. He was given separate directions for the characters, and had to piece it together himself that it was one person.
