The reasons for Cid's defection are twofold:

-He saw firsthand the brutality with which the Empire conducts war in Ala Mhigo, as he was present when Gaius took the city, and was appalled by it. (While the Empire took Ala Mhigo with little effort, it wasn't a bloodless conquest.)
-Solus decided that using Meteor was acceptable despite the devastation it caused at Bozja Citadel.

Just to clarify, I went and did research and I can't find anything stating that the Empire was responsible for catalyzing or magnifying Theodric's madness. Gauis did take advantage of the situation by having spies instigate the rebellion that led to Theodric's suicide, but the Empire was not responsible for anything prior.

I might dislike the Empire, but I dislike falsehoods even more. Not that I'm mad at anyone for believing as much, since I'm just as guilty.