The practice of Vedic animal sacrifices was opposed by Jains. Hemachandra, a Jain monk, cites passages from Manusmriti, one of the law book of Hindus, to demonstrate how, in light of false scriptures, Hindus have resorted to violence. Akalanka, another Jain monk, sarcastically said that if killing can result in enlightenment, one should become a hunter or fisherman."
I remember a grahapravesham ceremony in which the homeowner was asked to cut some lemons and place them in different directions from his new house as "bali" (to ward off evil influences, may be). It is likely that the lemon used to be an animal in olden days. Also the coconut that is present in most South Indian sacraments might be a replacement for the head of a sacrificed animal.