They allowed Cavill to announce, because the people in charge of DC at the time OK'd it and told him to announce; Cavill didn't do an anncouncement on their own without approval. They however, are not in charge of the new "template" that Safran and Gunn are in charge of and requires everyone to follow. And after planning around the last few weeks, Safran and Gunn do not have confidence in the ability to tell a story with established characters which aren't their own/or want to put their own stamp on things (A Casey Hudson Mass Effect 3 ending moment). So they want their own Superman and thus told Cavill to make a new statement about no longer being Superman.
In a way, not Safran or Gunns fault, but the point still stands; if they were good story tellers, they'll be able to salvage anything and tell a good story at the same time. Especially since there's good will towards Cavill in the role overall.