Does anyone think that the writers changed the outcome of the show because of all these theories?
They apparently didn't even have the story planned until season 3, so I guess it's a default yes. One of the creators said something like they knew what the ending scenes would be, but they didn't quite know how they'd get there. When they got their deal to end it with season 6, they apparently worked out the arc til its end, to some degree.
But like, there are other things to keep in mind, too. The Lost people said they had big plans for Mr. Eko, but well, shit happened.