No one could have known that COTEOF would become a classic episode
I don't think that's true. We now know from the TOS soundtarck boxed set that it was the only episode in which the score was recorded in full stereo. This suggests that it was identified right from the get-go as a classic, and deserved special care. I don't know why they would do this unless they thought maybe there'd be a soundtrack album, since TV was mono until the 80s.
It's also true that when people are passionate about something, they fight over it, not so much because they have to hate each other (although it can bleed over into that) but because they know their finger is on something awesome. The strength of this episode, despite every beef Justman highlights in his memo, was classic Greek drama in which the lead actor has to stand by and allow the love of his life to die. Heavy sh*t for 1960s TV. Edith Keeler getting hit by the car is that classic TV moment that will live forever, seconded with Kirk's tagline "let's get the hell out of here" which was the antithesis of the happy-ending bottle episode. They knew it would be one of the best episodes, regardless of the script revisions.