Neo necessarily wasnt killed by smith remember after all agents were deleted and we saw the oracle on the ground where smith was? well whats so different with neo?
I don't think he was killed. I think it's debateable, in any case.
But, I think he may have survived. I think the Machines are holding him. And I think he will return to the Matrix as a blind man, probably a beggar-type. He will have no power over the Matrix, because the code that made him The One was removed/destroyed by Deus Ex at the Source. But he'll return.
Probably around the same time that Morpheus returns.