To my knowledge, the first full-length version of the origin was the newspaper strip, and I don't think that included the Kents. They were first introduced in Superman #1, though they may well have been conceived of by the duo before.
The bit about Siegal's father is interesting. I must admit I'd never heard about it before. But is the extent to which it influenced his decision to have the Kents die during Clark's youth known? Has he discussed it in interviews as a critical element in his conception of Superman?
The Kents were originally not much more than a plot device to explain how Superman got his civilian identity of 'Clark Kent' and who raised this 'super-baby'. Its the Superboy stories that really made them supporting characters. So I don't think the issue of whether they lived or died was really that important to Superman's origin - certainly not to the extent of other core elements like Krypton exploding, or the infant Kal-El being rocketed to earth. No doubt their deaths were an important secondary story detail back then. But a lot of superhero origins have had such secondary details which have changed over time while the core elements stayed intact.
To me, Jonathan and/or Martha staying alive is a retcon akin to Alfred Pennyworth being the one to raise Bruce Wayne. It is a major change to the facts of the backstory, and it recalibrates the importance of certain characters to the ongoing narrative, but it doesn't fundamentally alter the hero's origin story.