I think it's pretty likely that what happened was:
The producers had the whole "they're all dead and in purgatory" idea early on. And the idea of the island as a magical place would easily explain everything in the first season (why Jack was seeing his dad, why people got 'better,' why babies could be born [because a fetus didn't have a soul]).
Then, way too many people guessed that purgatory was the answer. So, combined with the fact that they didn't know when the show would end, they switched gears and decided to go for a sci-fi theme. They probably figured, with guys like Brian K. Vaughn on staff, they could make the switch and come up with a satisfying sci fi ending that still ended with Jack's eye closing. They then spent a few years planning that out.
And, for a while that was also holding together because a lot of the stuff could to that point, also be explained with time travel and parallel dimensions.
Meanwhile, of course, real life intruded on whatever plans they were building. Walt got old. Ben became a fan favorite. The actors playing Ana Lucia, Libby, Jin and Desmond all had legal problems. There was a writers strike. These things forced unplanned rewrites.
Then, they got an end date and, as we got closer, they had more and more difficulties agreeing on an alternate ending. So they finally said "fuck it, let's go back to the purgatory thing, but we'll add a twist (Earth 2)."
So, in their mind it WAS planned all along, insofar as they went with their original idea. But also it was made up as they went along because they spent a few years with an alternate plan, trying to fill in seasons, accomodate actors, etc.
