No, Fatui were not rewritten. I have the actual hard evidence:
Liyue AQ, Childe's story quest, and the ending of the Mondstadt AQ. At the end of the Mondstadt AQ, Venti literally tells Traveler that Tsaritsa changed after the Khaenri'ah disaster, and he doesn't know what her goals are. Immediately after going to Liyue—in the main story quest, not some side mission—Traveler meets Childe, a Fatui Harbinger, and he directly tells them that not all Fatui are evil. And it's all 1.0 content. So no, Fatui were not depicted as pure evil in the beginning of the game. The whole Liyue story is us working with the Fatui until Childe unleashes the old god to lure out Morax, and it turns out it was all a setup between Zhongli and Signora. One of the ideas this quest tries to drive home is that the Fatui is not a monolithic organization, with Signora working behind Childe's back, and they are not mustache-twirling villains. And then there's Childe's story quest.
Why do you think the writers had us work with the Fatui throughout the entire Liyue Archon Quest? Why do you think Yae Miko gave away the Gnosis so easily? Why do you think Raiden was working with the Fatui during the Inazuma Archon Quest? Why do you think Raiden didn't object to Yae Miko giving away the Gnosis? Why did Zhongli give away his Gnosis? It was clear from the beginning what the writers were setting up.
Can people stop making up retcons about Fatui being pure evil from the beginning and actually revisit the content that's already been in the game from the start? I can bring up countless examples from 1.0 or 2.0 where Fatui are not depicted as pure evil.