I post this theory after i just read another that proposed that Aaron died, was infected, and resurrected while in the womb. Consider this similar but different.
I do not propose that Aaron has been infected, but rather present the possibility of his infection via another avenue.
Now to the theory...
Two scenes/stories have really struck me this season, and i believe them to be connected.
First is the Sayid/Clarie/infected storyline. I find it interesting that in death, assuming Claire is indeed dead, that the islands dark forces can claim/inhabit/infect and reanimate a body. MIB chose Locke, and i believe he has also claimed Sayid and Claire. It is entirely plausible that in the moments that following Rousseau's team's descent into the temple basement that they were all killed by Smokey and subsequently infected and reanimated with the dark forces.
The second scene that i believe is connected to the first is the opposite end of the spectrum and that is the Alternate birth of Aaron. "I do not want to needlessly inject him" (paraphrasing) - Ethan. Knowing Ethan's intentions and compassion, it is not too far-fetched to view the injections to Claire/Aaron while on-island as somewhat necessary.
What if the infection works similarly in birth as it does in death. The birth of child may be an avenue of infection for the dark forces. It would stand to reason that the moment of infection could only take place at birth, and not necessarily at conception, as children have been conceived on the island.
Could this be why Aaron was so damned important to the others?
Could this be the reason Claire was kidnapped and shot up with drugs (a serum that i have always felt was eerily similar to that which the Swan hatch inhabitants injected themselves with to avoid "infection")? Does Jacob / The Island know this and the result be a preventative measure that children can no longer be born on the island? Could there have been a child that was born infected/evil and suffered the same fate as past infected persons?
As we've seen and heard time and time again, certain actions are done for the greater good, and this may be a step Jacob/The Island is willing to take to ensure the infection will not spread. Also with the other's flaming-body-in-the-sea burial rituals, there would be little time for the infection to settle in on the dead mother (remember Sayid was out of it for quite some time before resurrecting.)
Lest we not forget Alex. Certainly the dark forces existed and were nearby during her birth what with Danielle killing her infected friends and all. Ben's orders were clearly to kill Danielle and Alex, but he let both live, then he claimed Alex in the name of Jacob which we all know now was a lie. Its not out of the realm of possibility that during this period the others were in fact following the lead of Jacob and Jacob knew it was possible that Danielle and Alex were infected due to Danielle's close calls with Smokey and his "army" and called for their deaths.