Just some thoughts a friend and I were batting about;
What if when it comes down to the wire, Jack is unable to detonate Jughead- maybe he bottles it, maybe Sawyer, Kate and Juliet stop him, whatever- and the Incident occurs, and the button is installed in the swan station as described in the orientation film (Yes, I subscribe to the Whatever Happened, Happened theory). Now suppose that, in the aftermath of the incident, rather than trying to move the bomb, Dharma bury it in concrete under the Swan station, and hook it up to the swans systems- specifically to the fail-safe key. They don't know if Daniel/Jack's plan will work, but they do it anyway. In 2004, when Desmond turns the fail-safe key at the climax of 'Live Together, Die Alone', he is in fact detonating Jughead, negating the energy successfully just as Daniel said it would.
Way back when they first got into the hatch, Sayid said the only time he had heard of concrete being poured all over something like that before was Chernobyl. Evidence?
Apologies if this has been theorised before. And also I have to give duel credit to my good friend Stewsith for this theory!