Well, I think they are still very important characters to how the rest of the story will play out...after all, it is Jacob's "game" that the candidates are trying to survive...and the rules of the game keep MIB from killing them himself. So, they are still involved.
The "light in the waterfall", is really just a different view of something we've been seeing since Ben first moved the island with the wheel. We always knew there were "pockets of energy" all over the island...and according to the series, elsewhere on Earth...but this is the only one that seems to control life/death (Rose's cancer being cured, Locke can walk, etc.).
There is still "something else", some other entity on the island that has yet to be revealed to us...plus we still haven't seen whatever original population was on the island, so there is still farther back to go. Whether they can get there...who knows.
But I know one thing, go back and watch season 1 and all this MIB/Jacob stuff was setup in that season even though we didn't know who they were yet.