A dead man's switch has been talked about already - I'd like to expand on the idea a little - linking some facts together.
A similar story was used in The Outer Limits once
DEAD MAN'S SWITCH
Ben Conklin (JAMES LE GROS) has been a loner ever since his parents died when he was twelve years old. This is one reason why General James Eiger (DONNELLY RHODES) selected him to spend a year buried in a bunker 11,000 feet below the Artic tundra, manning the controls of a doomsday device set up by world leaders after the Hubble space telescope spotted 11 spaceships heading towards Earth. The device is designed as a last-line deterrent against alien invasion and Conklin's job, shared with four other loners in four other bunkers, is to hit a dead man's switch on the bunkers control panel that prevents the doomsday device from going off and destroying aliens and mankind alike. At first, the job is easy, but as the aliens draw closer to Earth, and as Conklin grows closer to his subterranean colleagues, he begins to doubt the reliability of the doomsday machine. News from General Eiger becomes scarce, then Conklin's fellow guardians begin to fall victim to assorted mishaps. Conklin realizes that he carries the weight of the world - and the fate of mankind in the palm of his hand.
Now - if Desmond does get infected, he fails to enter the code - and something happens to prevent the spread of the 'sickness'. He did seem surprised that none of the plane crash survivors were not getting sick, so maybe the sickness has gone - however I think the sickness is there and People ARE getting sick.
What if the 'sickness' did not start out as a sickness at all, but an experiment into psychic ability or another level of mental being. Fo example, seeing ghosts, creating 'phantom' creatures etc.
However it was found that this does other damage and to be unstable and uncontrollable. A huge magnet was installed on the island for it's healing properties and to help 'channel' these abilities - a well known use for magnets. However this magnet also causes navigation equipment (on the island and nearby planes & ships) to go haywire.
Healing Magnets:
http://en.wikipedia.org/wiki/Magnetic_healing
The shots Desmond takes are just a preventative 'in-case' the sickness gets into the hatch - I know if i was down there I'd want a second fail-safe.
It will be interesting to see in the next episode when Desmond leaves the hatch if he starts 'seeing' things.
Anyone have any thoughts on this?