The Church of Light was obviously not prepared for the Roson Empire's actions. They did not know how to deal with the Roson Empire's counterattack this time. They had been used to the smooth sailing all these years and did not expect the Roson Empire to do this at this time.
In the beginning, they did not realize how terrifying this move was. By the time they realized it, it was already too late. Moreover, their relationship with the Roson Empire had never been too good, so it was too late for them to retaliate.
However, the Church of Light still retaliated. They retaliated in all the empires and duchies that were under their control. Of course, they were not stupid enough to retaliate against all mages. They only targeted The Black Mages.