(poss spoilers) was Fayt deleted in the end? even slightly? you can't survive deletion. really. deletion means you are completely erased from existence. you don't exist, you never existed, you never will exist. it can't be reversed. even by quoting Descartes. (/poss spoilers)
That's just the thing. When Fayt and the others, or rather their world, was created - it wasn't designed to have a consciousness. That was a bug, an error that arose as the game continued. The reason they were to be deleted was because they found a way to cross over to the creators dimension and materialize.
When they were deleted, their data was destroyed. The ending bases itself firmly in the practical application of a philosophy that the consciousness creates it's own reality. I think, therefore I am, you cannot destroy a consciousness by destroying it's reality - because you cannot destroy knowledge and thought, so the mind will recreate it's own reality to exist in.
This creates the problem that the reality we're presented with in the ending may only be the reality created by Fayt's consciousness - and may be completely different than the reality created by Sophia or Cliff's, or anyone else's consciousness. Unless, somehow, a reality was formed based on collective consciousness of everyone in that world. Or further, since their world was created as raw knowledge, which later gained consciousness, it cannot be destroyed since knowledge and thought cannot be destoryed, and that is all that they are.
Or perhaps that the "reality" dimension was in actuality just another level of programing in a far greater game. As in, you the player, playing a game controlling characters who are part of a game which exist in a layer between yourself the player and your characters... and so they weren't truly deleted.