How do you know that morality is God’s will if He did not command it explicitly?
When I keep the Sabbath, am I doing a moral act because I am fulfilling His command, and that’s it? If there is an essential conflict between religion and morality, then simply I would have to choose religion, because that is what God explicitly commanded, and when He commanded it He was aware of the moral problem and still commanded me to act that way, no? (As if there is not really any conflict, because if I say that the moral act is the right act, then if God commands me to wipe out Amalek, I must do so despite the moral prohibition, because wiping out Amalek is the moral thing, since God commanded it; if so, that is the right and proper thing to do. After all, the whole force of morality comes from the command.)

I know from my intuition. It says that there is valid morality, and there is no valid morality without God. Conclusion: He implanted it within us. The obligation to the Torah is also based on reason, as Rabbi Shimon Shkop also wrote at the beginning of Gate 5.
Therefore Jewish law does not have an inherent principled priority over morality, except where the clash is built in, as I have explained in several places in the past. Indeed, wiping out Amalek is an example of a built-in clash, and even so the commentators placed very strong limitations on it. Beyond that, the priority of Jewish law does not mean that this is the correct morality, but that in this case the Torah revealed to me that Jewish law overrides morality. I have discussed this at length, and there is no point repeating all of it here.

Why is it important to you to say that the priority of Jewish law is not the correct morality? What’s the problem if we say the opposite? In any case, I would be happy if you could refer me to the “places where you discussed this at length.”

It’s not important to me. It’s simply what is true. There are two series in my lectures on Jewish law and morality. There is material at the beginning of the third book in the trilogy, and a lot here on the site as well (for example, Column 15, and more).

David raises a good challenge, and rightly so, but I don’t see here an answer that confronts the problem head-on.
The confrontation first has to deal with the built-in problematic aspect within the Torah itself, according to which the values of the Torah and/or Jewish law take precedence over moral values (at least what Michi here calls “morality”), even if this clash is rare in practice.
This determination of the Torah—or at least what is hinted at in the Torah—is confused, or at least paradoxical, because in order for there to be a demand for principled priority of Jewish law, the Torah must assume the existence of universal moral principles that precede that very Jewish law… That is, there is a logical loop here.

For example, in the commandment to wipe out Amalek: on the surface there is supposedly a conflict between the religious command and its moral meaning (every person, including a Jew, knows that it is yucky to destroy old men, women, and children like that). Michi comes and says: indeed, there is a real conflict here, and in such cases the religious command must prevail over the moral one, even if it’s yucky.

That is an incorrect reading of the broader context. The “religious” command to wipe out Amalek rests on a purely moral principle: a person’s choices of which values/norms to adopt and which not to adopt are not “Torah-based” in any sense, but standard human choices. So too the choice to adopt this specific Jewish law/commandment. Therefore wiping out Amalek is not yucky at all (even if Michi’s psychology, or mine, tells us that it is). Now all that remains is to deal with the difficulty: why does the Torah insist on seeing this act as a distinctly religious command, meaning a principle that precedes morality, when even on its own view such a thing cannot exist?

Since I have never managed to get a substantive answer to this difficulty from Michi, I am directing the question to you, David.

From what I understood from Rabbi Michi, this is a semantic matter—namely, morality is what your intuition tells you to do (God did not innovate anything here; He only gives it validity), whereas religion is newly introduced commands from God. So when there is a commandment to wipe out Amalek (which is not a moral thing because intuition does not point to it), then it clashes with my intuition (morality) not to kill him. Whereas you define morality as the right and proper thing to do, and Rabbi Michi defines it differently. There is not really any disagreement here. (Correct me if I’m wrong.)

I didn’t understand how this matter of “innovation” helps. You too admit that there can be a contradiction between Torah and morality, regardless of how morality is defined—for example in the case of Amalek. So far, maybe there is no problem.
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But now the problem returns, and its logical form is not contradiction but paradox or a loop: according to the Torah, the command to kill Amalek precedes the moral obligation not to do so—that is, religion precedes what we have called here “morality”—but at the same time the Torah assumes the existence of moral values that enable the commandments to exist in the first place (including wiping out Amalek). Don’t you see a loop here?

I didn’t understand what the problem is. God commanded us about morality, and in certain situations He tells us to give up “morality” for the sake of more exalted goals. I don’t see any loop here. It’s a matter of clashing values, and the question is what overrides what. (It doesn’t even matter what came first.)

First of all, the question is not what God commanded us, but what the Torah says God wants.

Second, there is no such thing as specific values (what you called “more exalted goals”) without assuming the existence of a system of universal values that are not valid for certain situations but only in certain cases. This system is called morality, and it necessarily logically precedes specific goals.

Now the question is why the Torah nevertheless claims that there are specific goals that precede “morality.” After all, it too is logically bound to the principle I described, a completely opposite principle. In any case, even on its own view there is no more exalted goal than that which preceded it.