Pestilence's ring had been removed thanks to Cas and Ruby's knife. As the ring was removed from his body, the disease and sickness stopped like magic. It was the ring, after all, that had been causing everyone to feel as ill as they were.
The pile of dead Croats has dissapeared, along with a mass majority of those pesky flies. Though, the Croatoan virus had not been wiped off of the face of the map. Pestilence was not the only one producing that virus, in fact, Lucifer and his team of demons have a lot to do with it.
When your character's become concious, now that Pestilence is gone, it will be as if they never got sick. They will definatly remember the horrible feelings, but it will be a magical relief that washes over them.