I don't think that it has really vanished totally, as right now the audience is left unsure of whether the sickness was really real. The only one who seems to be sure that it exists is Rousseu. Desmond injected himself for years until he saw his partner go out with a rip in his hazmat suit and then later take it off. Was the whole sickness thing a method of control cooked up by Dharma. If so, why was Rousseu so convinced of it that she killed her whole crew (though maybe SHE was the one with the sickness, or she just went insane...).I think the disease subplot has all but vanished.
There are tons of side plots and unexlained mysteries that have been brought once or twice and then seemingly forgotten about about (like the damn foot statue!). But I agree with Ever Onward that the writers will come back to these threads in due time. It's just bloody hard to wait.