It was an incredibly small-scale infestation at the time which made it easier for it to be destroyed. Roland notes in Spartan Assault that Earth would've fallen in mere hours if Rtas hadn't glassed part of the continent, so we were lucky. Of course, the bit that still doesn't make sense in Halo 3 is the fact that the Gravemind just decided not to drop some Flood down to Earth when he went to go to the Ark through the portal High Charity can't fit through...