First, island occurences have bled over into the ATL, but we have yet to see anything from the ATL affect the island.
Second, I don't think the goal in the ATL is going to be preventing the happenings on the island from happening again. I think the ultimate goal is to stop Smokie on the island, possibly by sinking it, end of that story. Meanwhile, Desmond is working to bring everybody's consciousness from the island into the ATL so that they can go on with their lives aware of what they had been through.
In other words, I think once MIB is defeated, it is indeed ended and once the island is sunk, it will no longer need protecting (the light won't go out because the power is in the light and the water together). But if the characters went on in the ATL with no memories of the island, that would be a frustrating ending for the viewers, almost as if they did indeed all die. However, if Desmond is successful, they will be able to merge with their island lives and retain both, almost as if they had never died on the island. Life, death and rebirth.