"Eyes to See", R' Yom Tov Schwarz, Urim Publications: Product page with reviews
Rabbi Schwarz first brings the famous story of the sufferings of Rabbi Yehuda haNasi (colloquially called simply "Rabbi" or "Rebbe"), in Baba Metzia 85a. According to the Soncino translation (I have chosen this in order to minimize how much I must type myself):
'They came to him through a certain incident.' What is it? — A calf was being taken to the slaughter, when it broke away, hid his head under Rabbi's skirts, and lowed [in terror]. 'Go', said he, 'for this wast thou created.' Thereupon they said [in Heaven], 'Since he has no pity, let us bring suffering upon him.'
'And departed likewise.' How so? — One day Rabbi's maidservant was sweeping the house; [seeing] some young weasels lying there, she made to sweep them away. 'Let them be,' said he to her; 'It is written, and his tender mercies are over all his works.' Said they [in Heaven], 'Since he is compassionate, let us be compassionate to him.'
 - Ps. CXLV, 9.
Rabbi Schwarz then asks (to paraphrase), what should Rabbi have done instead? Surely, he should have slaughtered this calf for his needs; should he have spared its life? And surely G-d has indeed permitted us to slaughter meat for our needs. So what did Rabbi do wrong?
Rabbi Schwarz offers two answers to this question (again, pp. 115-117):
Numbered notes (  etc.) are Rabbi Schwarz's; lettered notes ([a] [b] etc.) are my own:
However, the truth is that the incident with Rebbe does not pose any difficulty whatsoever, since the question we have raised can be answered in two ways. First, when the Torah sanctioned the slaughtering of animals and allowed us to disregard their suffering, it was only in the case of ordinary animals and birds, for they do not have the intelligence to realize what is about to transpire before they are slaughtered, so that they suffer no pain and anguish prior to their slaughter. The actual pain of the slaughter itself is something we need not be concerned with, since G-d has expressly permitted us to do so.[a] However, in this particular incident, Rebbe could see with his own eyes that something extraordinary was happening: this calf realized it was being led to slaughter, and seemed to be suffering greatly from this and begged Rebbe for mercy. In this case, he should have exercised compassion and refrained from slaughtering the animal. For under these extraordinary circumstances, perhaps the Torah indeed prohibited its slaughter, on grounds of cruelty to animals.
Furthermore, Rebbe should have reasoned along these lines: The Torah instructs us, "And you shall slaughter, and you shall eat," and we must certainly not question the Torah's justice ch"v [chas v'shalom or chas v'chalilah, i.e. G-d forbid], for "the ways of Hashem are just"  and contain no injustice. However, this is not to say that there is no basis whatsoever for feeling compassionate towards this animal. In fact, if the Torah had not sanctioned slaughter, we would not have been able to permit it on our own accord.[b] However, by expressing himself in this manner - "Go! It was for this that you were created!" - it appeared as if Rebbe was saying, "There are no grounds for being compassionate towards you, and not slaughtering you and eating your meat. For you were created for human consumption, and are no different than vegetables and other grains." [I.e., Rebbe was overly unequivocal.] This is why he was punished with afflictions. For in truth, we are obligated to be merciful on all living things. Thus, the Talmud teaches (Gittin 62a): "Said Rav: It is forbidden for a man to taste anything, until he first feeds his animals. For the Torah states, "I shall provide grass in your field for your cattle," and then 'you shall eat and be satisfied.'"
 Hosea 14:10
 Deut. 11:15: The order of this verse indicates that G-d wants us to feed our animals before ourselves.
[a] However, G-d did require us to minimize the pain as much as possible, such as via the method of shehita, involving an instantaneous loss of consciousness to the animal, due to the instant and spectacular loss of blood pressure to the brain.
[b] In fact, G-d forbade the consumption of meat, and He permitted it only later, to Noach. Now, G-d's permission there appears to be a non-sequitor; He forbids murder, and then permits meat. Sefer haIkkarim (according to the citation in Rabbi Yehudah Nachshoni's Studies in the Weekly Parshah, Parshat Noach) explains that G-d wished to underscore the prohibition of murder, and accent the sanctity of human life, by permitting the slaughter of animals in direct connection with the prohibition of murder. Moreover, says Sefer haIkkarim, since man, before the Flood, had engaged in bestiality, G-d needed to still yet more emphasize the gulf between man and beast, adding force to his explanation. Alternatively, more metaphysically, but along similar logic, Rav Kook (as quoted in Nechama Leibowitz's famous Studies in the Weekly Sidra, the volume on Bamidbar I believe) explains that G-d wanted man to be able to concentrate all his ethical energy on his fellow man, and not have to focus so much on animals; by permitting us to have some cruelty and bloodthirstiness on animals, by consuming them, we thereby have more energy to expend on our fellow man. According to either, the permission to consume meat is highly grudging, and Rav Kook says that in the Messianic era, animal consumption will cease, and even the Temple will have no animal sacrifices. (Rav Kook based this primarily, if I remember correctly, on the belief that when "the knowledge of G-d will fill the earth as the waters cover the sea", this will apply to animals as well as to humans; animals will rise to the level currently held by man, and man will rise to one level beyond his current level. I recently saw in Rabbi Marc Angel's Rabbi Haim David Halevy: Gentle Scholar, Courageous Thinker, that Rabbi Hayim David Halevy independently arrived at the notion that in the Messianic era, there will be no animal sacrifices at all. He based this on the fact that the sin and guilt offerings will be no more. Now, he realized that other sacrifices will continue, and that these sacrifices would presumably continue to be meat. Nevertheless, Rabbi Halevy was confident that there would be no more animal sacrifices at all, even if he couldn't prove it. He himself was gratified when he later discovered that Rav Kook had expressed a similar teaching.)