All religious (or potentially religious) Jews have difficulty with mitzvot which seem to be outdated. How can a thinking Jew understand & identify with a Torah which allows slavery, bigamy or taking enemy women during war? This class also deals with many questions raised by women or feminists regarding the role of women in Judaism, laws of Aguna, divorce, the brachot of "Shelo Asani Isha" or "SheAsani KiRtzono", etc. Rav Kook, one of the most innovative & brave Gedolei HaDor, writes a lot on this issue of "updating", explaining & identifying with the Torah in a totally Orthodox way (on which no one can disagree), to bring the Torah closer to all. [It is the 1st part of the class on "Mitzvot Which Seem Immoral", also highly recommended!].
Every moral & thinking Jew has asked questions about certain mitzvot which don't seem to "jive" with the morality of God & the Torah itself! Rav Kook, as usual, bravely deals with these issues, & explains that "eternity" means that the Torah also had to be relevant to the primitive world in which it was given 3,300 yrs. ago. He differentiates between some actions, like slavery & bigamy, that had to be "allowed" temporarily in the ancient reality, but were never obligated. Nevertheless, 2 obligations (!) which seem "immoral" are regarding Amalek (killing & remembering-Zachor), & conquering the Land of Israel. But upon a closer look, they aren't immoral at all! When we lack prophets & Sanhedrin, the God Who runs History solves many problems!
The Mitzvot include both Mishpatim (understandable) and Chukim (non-understandable). Rav Kook posits that the differentiation between the two is consciously unclear, because study turns the Chukim into rational, and society sometimes interchanges what was thought as rational into a chok (e.g. homosexuality may be seen differently, but it's always wrong).