First of all, he says: that’ll be the day that you leave me. One common meaning of “that’ll be the day” is “it will never happen”. The listener hears this as implying that his partner would never dare to leave him. She will stay forever. There are several lines that imply this.
And then with the words “… that I die” the meaning suddenly shifts. It now becomes a desperate plea not to abandon him.
I think when someone says “that’ll be the day” it means “vey unlikely” no matter how the phrase ends. “when you say goodbye” is not the end of the thought, though. it’s just a clause on the way to the conclusion, which is “when I die”. It’s vernacular and pretty clear to me. I don’t get the sense he is saying anything else. It’s got humor and a taunt in it.
I’d never interpreted it as anything but " as if"( good comparison, Shoeless), especially the Linda Ronstadt version, but I can totally understand the other explanation. What a good question!
In high school I told a classmate I’d kill him. He said, ‘On, yeah? The day that you kill me will be the day that I die.’ I don’t think he thought it through.
It’s quite interesting how “The Searchers” penetrated the music of the time. In addition to John Wayne’s line making it into the Holly song, the Searchers of “Needles and Pins” fame took their name from the film, and “Searchin’” by the Coasters did the same!