Why did ADVENT kill all domesticated animals?
Most often extraterrestrials are identified and alerted to owners by domesticated animals, like dogs, cats, parrots, etc.
Since Advent has actually become a surrounding of people but in a way to sway their alertness, it sounds as normal act to prohibit anything that would go against them or serve as base for rejection.
Feeding species with its own remains (in any form) has proven to be overly bad idea, for example mad cow diseases, and I would expect the same for humans (let's not go into topic of cannibalism yet). Except if broken down to prebiotic soup and syntethizing something from that.