The Vedanta Sutras of Badarayana, Commentary by Sankara (SBE38), tr. by George Thibaut  at sacred-texts.com
25. Should it be said that (sacrificial work is) unholy; we deny this on the ground of scripture.
We proceed to refute the remark made by the pûrvapakshin that sacrificial works are unholy because involving harm done to animals, &c., that they may therefore lead to unpleasant results, and that hence the statement as to the souls being born as plants, &c., may be taken in its
literal sense; in consequence of which it would be uncalled-for to assume a derived sense.--This reasoning is not valid, because our knowledge of what is duty and the contrary of duty depends entirely on scripture. The knowledge of one action being right and another wrong is based on scripture only; for it lies out of the cognizance of the senses, and there moreover is, in the case of right and wrong, an entire want of binding rules as to place, time, and occasion. What in one place, at one time, on one occasion is performed as a right action, is a wrong action in another place, at another time, on another occasion; none therefore can know, without scripture, what is either right or wrong. Now from scripture we derive the certain knowledge that the gyotishtoma-sacrifice, which involves harm done to animals (i.e. the animal sacrifice), &c., is an act of duty; how then can it be called unholy?--But does not the scriptural precept, 'Do not harm any creature,' intimate that to do harm to any being is an act contrary to duty?--True, but that is a general rule, while the precept, 'Let him offer an animal to Agnîshomau,' embodies an exception; and general rule and exception have different spheres of application. The work (i.e. sacrifice) enjoined by the Veda is therefore holy, being performed by authoritative men and considered blameless; and to be born as a plant cannot be its fruit. Nor can to be born as rice and other plants be considered analogous to being born as dogs, &c. For the latter birth scripture teaches with reference to men of evil conduct only; while no such specific qualification is stated in the case of vegetable existence. Hence we conclude that when scripture states that the souls descending from the moon become plants, it only means that they become enclosed in plants.