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As I discuss in this question, by far the most popular school of Hindu philosophy is the Vedanta school, which bases its tenets on the doctrines laid out in the Brahma Sutras, a work by the sage Vyasa that summarizes and systematizes the philosophical teachings of the Upanishads. You can read the Brahma Sutras here. In any case, Vyasa discusses the issue of animal sacrifice near the end of Adhyaya 3 Pada 1 of the Brahma Sutras:

  1. If it be argued that rites (invoking killing of animals) are unholy, we say, no, since they are sanctioned by scriptures.

And all the commentators I have come across take this to be a statement that animal sacrifice is not immoral and does not generate bad karma. Here is what Adi Shankaracharya says about this in his Advaita commentary on the Brahma Sutras:

We proceed to refute the remark made by the pûrvapakshin that sacrificial works are unholy because involving harm done to animals ... 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.

And here is what Ramanujacharya says in the Sri Bhashya, his commentary on the Brahma Sutras:

it is not so, on account of scriptural statement. For Scripture declares that the killing of sacrificial animals makes them to go up to the heavenly world, and therefore is not of the nature of harm. This is declared in the text, 'The animal killed at the sacrifice having assumed a divine body goes to the heavenly world'; 'with a golden body it ascends to the heavenly world.' An action which is the means of supreme exaltation is not of the nature of harm, even if it involves some little pain; it rather is of beneficial nature.--With this the mantra also agrees: 'Thou dost not die, thou goest to the gods on easy paths; where virtuous men go, not evil-doers, there the divine Savitri may lead thee.' An act which has a healing tendency, although it may cause a transitory pain, men of insight declare to be preservative and beneficial.

And here's what Madhvacharya says in this excerpt from his Dvaita commentary on the Brahma Sutras:

It may be said that sacrificial work involves injury to life, and as such it is productive of sin and consequently of misery, and that, therefore, it is not to be performed. But this objection is to be refuted on the ground that the injury to life involved in holy duties is permitted by the word (scripture); for the Varahapurana says, "To do harm to any life except as enjoined by scripture is really productive of sin and evil consequences; on the other hand, no evil consequences possibly arise from the act of killing permitted by the Vedas."

And here's what Baladeva Vidyabhushana says in this excerpt from his Gaudiya Vaishnava commentary on the Brahma Sutras:

Because piety and impiety is known only from the Vedas’ statements, the Vedas’ order to commit violence must be understood to be actually kind and pious. Therefore the orders of the Vedas are never impure. The prohibitions “Never commit violence to anyone,” and “Violence is a sin,” are the general rules decreed by the Vedas; and the statement, “One should sacrifice an animal in an agnisomiya- yajña,” is an exception to that general rule. A general rule and a specific exception to that rule need not contradict each other. There is scope for each. For these reasons, therefore, the scriptures’ description that the fallen soul takes birth as a rice plant or similar being is metaphorical and not literal.

So my question is, are there any commentaries on the Brahma Sutras that interpret this Sutra in a different way? Or do all the commentaries agree that this Sutra is a statement that animal sacrifice in Vedic Yagnas is not immoral/does not generate bad karma?

I suspect that all or almost all the commentaries are in agreement on this point, which makes it all the more strange that a lot of modern Hindus believe that animal sacrifice is unequivocally immoral, especially considering that almost all Hindus belong to sects which subscribe to the Vedanta school of philosophy, and the Brahma Sutras are the defining text of the Vedanta school.

  • All of the commentators I have seen have said it can be done, because Veda is Veda is Veda. Having said that, like the horse sacrifice, it can be done also through meditation rather than an actual sacrifice. – Swami Vishwananda Jul 29 '15 at 10:56
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    I would like to draw explicit attention to the fact that while animal sacrifices themselves may not be condemned according to the sutra, clearly most of the current day animal sacrifices are deficient in procedure, purity and purpose and are therefore unequivocally voiced brutal. When pure Brahmanas perform such sacrifices as Agnisomiya, no real violence is caused to the animal (Agnisomiyaadishu cha na himsa pasoh). The Yajur Veda (4.6.9.46) declares that the animal will pass through the happy paths to the realms of the demigods such as Savita, where the pious alone reach and not the sinful. – rk567 Jun 13 '17 at 22:48
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    @rk567 Yes, animal sacrifices performed today are Tantric animal sacrifices, not Vedic animal sacrifice. The Brahma Sutras are talking about Vedic animal sacrifice, which no one does anymore as far as I know. – Keshav Srinivasan Jun 13 '17 at 23:54

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