> For example, many pit bulls who attack or maim people these days get put down by animal control. If a court could prove that an animal had been trained/conditioned (by a proven guilty defendant) to commit the offending act, would said animal still be facing death?

Yes, putting down a dangerous animal isn't a criminal punishment premised on the animal's culpability (as a matter of law, animals lack the capacity for culpability), but a protective measure equivalent to condemning and demolishing a dangerous building.