Actually, he probably had a good idea of the Didact's intentions. When Chief first awakens the him, the Didact goes on a long rant about how he hates humans and it isn't too late to stop them from claiming the Mantle. And didn't the Librarian talk to him about what the Didact plans to do? He may not have known the specifics, but he knew that the Didact's goal was the destruction of humanity.