Happy to say I've still not seen the film and am avoiding the spoilers at least until it appears for rent in Spar, so this is just an opinion.
I think Mr Smith has a significant role to play on the grounds he seems to be fighting everybody, intent on the destruction of everything and getting stronger! There is also the broader deeper biblical meanings behind the story.
If Neo destroys the Matrix, it will restart as bigger and better. In the process it destroys the free humans. It may be a case that Neo must become the Matrix to recreate it. But we then have the Smith factor that can no longer be controlled. Which ever way- Neo loses, possibly with a side order of the destruction of the Matrix
If Neo is destroyed. The Matrix destroys Free humans. Without Neo there is no balance for the destructive influence of Smith the Matrix is destroyed. Everybody loses
If Neo does not destroy the Matrix and he is not destroyed, then the Matrix will concentrate more and more resources upon the 'Free' humans, ultimately resulting in their destruction, whilst Neo is fiighting an ever more powerful Smith. The destruction of the 'Free' Humans will ultimately end in the destruction of the Matrix as there is no where for stray variables to go. Either way. Neo loses.
If Neo surrenders himself for peace. The Matrix can combat Smith effectively neutralising him. Because the Matrix has not been restarted. Neo can continue, if in name only, as a faith (ala christianity?). The Matrix has not been destroyed, but now has to accommodate 'Free' humans, time will then bring on the orderly dismantling of the Matrix. Neo wins