A Dance with Dragons discussion (SPOILERS!)

[Cor Azer]

See, and I simply assumed they were the bodies of the hostages.

I don't recall if there was a particular passage that solidified my idea, but I think it cones down to Selmy's soldier dispassion - he was never really close to any of the hostages, but sees protecting the city for Dany as his duty, and while an encamped army is an enemy he knows (even if difficult to fight), citywide disease was always a matter for septons and maesters - definitely outside his skills and training.