I still think the the Flu was engineered by the Governors buddy (Milton?) who was experimenting on the walkers on the earlier season. That group of people was infected and left behind knowing that Rick would take them in.
I also think that the person feeding rats to the walkers is the little girl who was upset that the walker with the "Erick" name tag was dead right after her dad died.
I agree that the person feeding the rats is probably one of the kids.
I don't think that Milton had the medical or scientific knowledge to develop a strain of flu and/or isolate it and infect a target population. Especially with something that wouldn't show until 6 months after infection.
There are walkers outside of the wire that show signs of the flu.
Dave