What is the conflict between Cudgeon and Root in planning the first siege against Artemis?

Lieutenant Cudgeon is the leader of the Squad. He and Root had been in the Academy together and they discuss what they should do in this situation. Cudgeon wants to use a blue rinse, a biological bomb that destroys all living things. Cudgeon believes that the blue rinse will cause a minimum loss. Root doesn't like this, as it will also kill Holly which Cudgeon states won't be a problem to justify. This comment makes Root turn purple in rage and he insults Cudgeon who calmly tells Root the rules in the Book that must be followed. Root winds up apologizing.