I can’t imagine they got McDiarmid to redub (and match the animated lip sync) on six seasons of The Clone Wars. Plus, with how highly Dave Filoni has spoken of the late Ian Abercrombie in the role, I don’t believe he’d go along with erasing that performance.
As far as changes go, this was a pretty “easy” one to make. It’s a single scene, there’s no lip sync to match, and they can even go get Witwer’s blessing if they felt so inclined. It also makes it match up better with Palpatine’s later appearance in Season Four. I don’t love it, but I also understand the inclination to do this.
EDIT: What I could see, though, is them getting McDiarmid to voice Palpatine for the upcoming final batch of Clone Wars episodes coming to Disney+. If they already got him in the booth for that, it’d be easy enough to have him read this one scene from Rebels.