remember the aptly named dharma initiative with all their experiments concerning parapsychology, life extension, and theoretical physics? perhaps they knew that the power source of the island could be harnessed to transcend to an undefined, higher layer of consciousness.
it's already been theorized by others that the flashsideways/"purgatory" was created during the incident, as heavily suggested by the screen dissolving to white as opposed to the familiar cut to black. it's already been theorized that this alternate reality was willed into existance by all the crash survivors wanting to change their fate, by wanting to the plane to have landed safely in los angeles.
as many have pointed out, the "church" contained symbols of all major religions. in other words, the church and other religious imagery were the result of the characters' ideas of higher planes. in other words, they were symbols to express an realm they didn't exactly have a word for, a la joseph campbell.
perhaps the characters transcended to this realm (or even willed it into existance) so that they could once again cross paths and then experience a rebirth together. it ties in nicely to the show's major themes involving destiny.
though the purgatory explanation works, it doesn't take into account the obvious buddhist and egyptian imagery the dharma initiative was so fond of...
long story short, the dharma initiative was more than just a plot device or macguffin, as so many of began to think at the beginning of the final season.