Unless Hershel actually witnessed the "killing", which is unlikely, his statement is based on speculation only.......
At that time, there were other members of the prison who were starting to exhibit symptoms of the "New Flu" so why would Carol just arbitrarily kill Karen and David?
And since they were both dragged from the same cell block, assuming they were both still alive, it would be an extreme feat for Carol to kill one of the two without the other attempting to come to the rescue and put up a struggle.........
And as a side note, don't forget, Carol suffered the disappearance of her own daughter Sophia, only to see her zombie-killed at Hershel's farm when the the barn doors were opened........
In episode 2 “Infected” the only ones who had exhibited flu symptoms were Patrick, Karen, David, and the pigs/boar. Carol killed Karen and David and burned their bodies hoping that she could contain the sickness. But, her plan didn’t work as we saw in last night’s episode when others started showing symptoms, too.
I think Carol doesn’t want a repeat of what happened to Sophia, so that’s why she’s been teaching the kids how to use knives, etc.