Nimoy saved Naked Time then, because without that scene, it's pointless. I'm not sure what JDFB thought he was protecting.
According to Nimoy's autobiography, it wasn't that John D. F. Black thought he was protecting the script as originally written. Rather, they were making TOS at break-neck speed, and all of the writers were frantically writing and re-writing as fast as they could. (You probably know that they often filmed a scene mere moments after the pages for that scene exited the writer's typewriter -- one has to have a lot of respect for the actors' ability to memorize their lines so quickly!) So what Black was protecting was his TIME, his ability to work on the next script, because "The Naked Time" was supposed to be done, already.
I can sympathize with Black's exhaustion and his need to go on to the next script, even as I agree with you and with Mr. Nimoy that it was crucial that Nimoy stepped in and got this scene fixed.
