This is more of a hope than a theory but this is how I think it will end.
Only the successor of the smoke monster can kill it with that wierd knife in particular just like how MIB killed mother from behind, John Locke is so badass just when MIB is about to win and destroy everything he will come from alternate universe and throw the knife in the back of MIB just like how he killed Naomi once again facking up everyone's shiz and giving the biggest WTF moment in television history.
We all know deep down inside all this hype around Locke since the beginning about him being special, the chosen one (just like MIB) can't have ended with Ben killing him. Desmond has always been the failsafe in the whole plan and can't be the smoke monster because of his resistance to electromagnetism, he is also the fail-safe for real Locke as he will bring him back.
It's clear the John is the successor to the MIB. The whole Knife thing is so esque of Locke, he even picks it as a kid when Richard gets disappointed, because he knows that the Knife will be more important to him in his destiny. He draws the smoke monster as kid, he just "knows" certain things like MIB, likes to play backgammon similar to senet which MIB found.
For God so loved the world that he gave his only Son, so that everyone who believes in him might not perish but might have eternal life.
– John 3:16 (New American Bible)
You just got to believe in Locke, hence the note before he died "I wish you had believed me". Doubting that he'll save the day is foolish, don't you know the number 1 rule of Lost is that you should never EVER tell John Locke what he can't do. Number 2 he fuck up everyone's shit like he does every season, this can not be avoided.
http://www.youtube.com/watch?v=vqruY6tlay4
This scene is extremely like MIB and Jacob scene, it has always been Locke and Jack as the two new protectors of this island. This is how the rivalry between the two has emerged from the beginning, they both have different beliefs just like MIB and Jacob keeping the island in balance.