I can think of three interpretations of what it means to be "infected". Which do you think it is?
A. Infected means that Smokey/MIB is slowly working his way into you. He did a big-time takeover with Locke, but usually he works more insidiously. The water isn't clear in the Temple because Smokey somehow found a way to dissolve himself in the water, and now he's infected the dead Sayid to take him over too. Probably Claire died somehow and then Smokey infected her too.
B. Infection is actually an infection - biological or energy or some other non-sentient force. It spreads into humans and changes their behavior.
C. Infection is the result of another third party, neither Smokey/MIB nor Jacob, but a third entity of which we know fairly little yet. This entity infects dying humans (unlike Smokey, who just inhabits bodies of the dead) and causes destructive and violent anti-social behavior.
If it is A, then why doesn't Dogen and Lennon just tell Jack "Smokey has taken over your friend Sayid"? Jack knows that the Smoke Monster exists.