The comments have been misleading. The show's creators have been very clear about the fact that they were not dead the whole time, only during the flash-sideways in season 6. The explanation given on the official podcast by Damon Lindelof and Carlton Cuse for what Jack says is simply that he isn't an anthropologist, or archaeologist, so he misjudged the age of the clothes by about 2000 years.
I, for one, don't quite believe this explanation, and I think it's simply that the original vision for Adam and Eve was for them to be characters from a much more recent time, and Jack's estimate was originally intended to be accurate. But, later on, the story took a different direction.