The FBI's backup in this case to Apple agreeing to work with them might just be to force Apple to disclose their signing key for iOS disk images, which could potentially be worse since it would enable the FBI and not Apple to control on which device(s) the image was installed. From a PR standpoint, that might be better for Apple since they could argue that they did not cooperate in creating a bypass, but from a technical perspective, it would be much worse.

Were I in Apple's position, I would probably do what Apple is doing here... but it's a harder question than just "should we cooperate?" They have to ask, "what if we don't?"