I have heard that Rav Kook felt that there may not be animal sacrifices in the Third Beit HaMikdash. How does this "jive" with the eternity of the mitzvot that they will never change? What will we do with the book of Vayikra (Leviticus) which speaks so much about animal sacrifices?
Rav Kook (Ktav Yad Kodsho II, pp. 15-17) relates to both possibilities: that animal sacrifices may return in the Third Beit HaMikdash (the historically mainstream opinion, see Rambam, Mlachim 11, 1), or alternatively, he proposes possible halachic justification if the Sanhedrin may prefer (either temporarily or permanently) to annul them. The bottom line is that he leaves all the options open, and if the Sanhedrin may feel that having animal korbanot may "turn off" people from wanting the Beit HaMidash (maybe even temporarily), he suggests several different halachic ways to justify such an approach. He obviously takes into account the halachic “given” that the mitzvot are eternal, yet nevertheless, suggests ways to solve such issues. There are many chapters in the Torah which don't apply today and apparently won't apply ever again in the future. For example, all of the laws of slaves, Amalek no longer exists, the 7 nations of Canaan no longer exist, according to many opinions the lost 10 tribes are not going to return (and accordingly, shmitta, yovel, trumot and ma’asrot will never return m’d’oraita, etc., etc). This does not at all contradict the principles of faith, for it does not mean to say that those mitzvot are not eternal, chalila, but that the conditions which warrant or enable those commandments no longer apply. Theoretically, if we were to find the 10 lost tribes, everyone would agree that those mitzvot would again be practiced. Similarly, Rav Kook writes, among other points, that mankind is continuously undergoing moral evolution and improvement, and that eventually we will return to the ideal original standard of Adam and mankind who were vegetarians before the Flood, where afterwards God only “begrudgingly” allowed man to eat meat (Breishit 9, 3). Accordingly, at that time (it may not be that far away…) man will no longer want or need animal sacrifices, because we will sin less, and not need sin-offerings. Additionally, the korbanot are called: “lechem, ishei rei’ach nicho’ach”- but when mankind no longer will eat meat, then animals won’t be considered “lechem” (=food) any more; if mankind will be disgusted with the smell of meat, then it won’t be considered “re’ach nicho’ach” (=a pleasant fragrance) anymore, so that even if one would bring a korban at that time, it won’t be a mitzvah, because the conditions no longer apply. Just like the mitzvah to enjoy meat on Shabbat and Yom Tov doesn’t obligate a person who does not enjoy them. He adds that perhaps all of the mitzvot of animal sacrifices apply only when the kohanim serve in the Temple, but according to many sources that in the Third Temple, the firstborns will return (as before the Cheit haEgel- Sin of the Golden Calf) to join the kohanim in the service, then all of the “ground rules” and premises may change. In short, the mitzvah is eternal but the conditions of fulfillment are not. Rav Kook adds that this may be the meaning of the pasuk we recite every day: “וערבה לה' מנחת יהודה וירושלים”, “(On that day) the vegetarian offering (=“minchat”!) of Judah and Jerusalem will be desired by God” (Malachi 3, 4). As I mentioned, Rav Kook himself writes all of this only as a possible and theoretical halachic justification if (!) the Sanhedrin should opt in this direction, for all agree they can halachically annul any mitzvah (Hil. Mamrim 2, 4) especially through passivity, (“שב ואל תעשה”) or innovatively deducing the Torah differently (ibid, 2, 1, possibly along the lines of the aforementioned suggestions). Rav Kook is obviously just as knowledgeable and worried about fulfilling the mitzvot and their eternity as you and I are, and precisely because of his intense belief in the truth and eternity of the Living Torah and the prophecies, he constantly tries to see the Ge’ula redemption though the mature “lenses” of realistic practicality and relevance, and not as kindergarten fables. The Tanach and her prophecies have been coming true over the last century, often through technological and historical surprises that no-one could have imagined before. Just as airplanes are "flying" (Yishaya 60, 8) the exiled Jews back to Israel from the four corners of the world; medical advancements are enabling childbirth without pain; 99% of the barren can now conceive; most of the previously-thought blind and deaf can now hear through cataract and other surgery and hearing aids; computers bring extensive Torah knowledge to the fingertips of the masses; air-conditioned tractors enable plowing without sweat, etc. Historically, nobody foresaw the collapse of the former Soviet Union nor the holocaust, but those who “saw the writing on the wall” and were pro-active to come on aliya and aid others to do so, hastened and implemented God’s historical plan. The historical God of Israel brought non-religious pioneers and a non-religious Eliezer Ben-Yehuda who side-stepped the rabbis and revived God’s deserted Holy Land and Holy Language without waiting for the rabbis to settle their debates on these issues. Rav Kook encouraged all of the aforementioned developments, and feels the same regarding this issue as well: we must think creatively, practically and realistically how to implement the Third Beit HaMikdash in a way which will be relevant to all of modern Israel (not to ancient Israel and not just for religious Israel). In addition, please note, much of Sefer Vayikra still does or can apply. In addition, allow me to point out that kabbala offers many additional hidden aspects to the Torah (perhaps you have heard, for example, of the hidden codes through letter-skipping, which are now easily available to everyone with the God-sent computers) where many ideas and even significant historic messages are hidden inside and in-between the words). This (and who knows what other new methods of study, computers will bring us in the future…) opens our eyes to entirely new ways of learning and utilizing those parshiot which no longer have practical ramifications, like much of Vayikra, the many names of the stops in the midbar (desert), the repetitive parshiot, the detailed names of the descendants of Esav, etc. The Zohar is full of other symbolic ways of learning the words of these parshiot, as well. With Love of Israel, Rav Ari Shvat