I originally posted a theory on the MiB's page about him being killed by water at the start of Season 6. Given that we've now seen Flocke interact with water on a number of occasions, this theory was updated to state that he is "affected" by water. See the theory page for the details.
I'm still of the belief that water is ultimately his weakness and, in smoke form, it could kill him. If this is true, this gives a reason why the island would be sunk... as a last resort if containment failed. I don't accept that the bomb was how the Island was sunk - it would, at most, rip the Island to shreds. The first Episode of Season 6 shows the Island seems to have been lowered quite smoothly.
However, it's clear that - by the time he got off the island - it would be too late to do something about it. However, not if the Island was sunk back in 1977... before he found the loophole. Given Desmond's uniqueness, he would be the ideal candidate to go back and do this. Whereas everyone else that turns the wheel is thrown off the Island, he may be able to stay there - but just go back to 1977.
Note that the Island was Sunk, not necessarily destroyed. There is the possibility that it could be refloated 30 years later, and maybe that is what Desmond is trying to do in reassembling the Losties.
Also, what is the extent to what Desmond can see into the other timeline... can he see the conclusion of both, and know what is to come?