I'm thinking it's not the light that will stop MIB but the water. He has a problem with water. So if they can trap him somewhere like a cave where they can flood it with water, that should do it. Gee, too bad they can't figure out a way to sink the whole island.........wait a minute......... 
But wasn't smokey residing in the light cave (filled with water)? Smokey has also been seen in the rain. How do we know he is repelled by water?
We don't know for sure if Smokey was in the cave and released when MIB went in or if MIB 'became' Smokey (another mystery!). I read spoilers last week that said this episode would show us how Smokey was 'created', so I'm going on that clue and assuming that this was the first time Smokey existed.
As for the water, we were given the impression that Flocke couldn't fly over to the other island as the smoke monster to kill everyone, that he had to go over in physical form. There's been debate that Smokey is somehow 'tethered' to the island and he may only be able to leave in a physical form. This got me thinking that the purpose of sinking the island would be to trap him once and for all. With no phsical means to leave, and the inability to travel over or through water (remember Ben's lame drain plug scene) Smokey would be trapped or killed on the submerged island. Also, the idea that he can't die and would just be trapped leaves open the idea that he somehow could escape if the island ever rose again. Imagine a dive expedition in the future where someone thinks they've found Atlantis and they inadvertantly provide Smokey with a way to 'come up for air'. I hope they don't leave the show on a cliffhanger like this, but who knows, they may decide to make a movie instead after all!
