Does halakha really prevail in practice over morality?

I know the rabbi spoke a lot about the relationship between halacha and morality. Bottom line in conflicts where halacha explicitly instructs against morality, it will prevail (from what I understand). But I want to speak practically, would the rabbi agree to have a person executed for desecrating the Sabbath? Having sex with a man? Or any halacha that completely contradicts our conscientious morality assuming we have no interpretive explanation that saves us from doing so? I really don’t get it. These are the kinds of things that always cause me real disgust, and I know that this is not a consideration but simply a sharing of the experience of frustration that I see no way out of.
The argument of “the people of Israel are not there yet (on the spiritual level) and we don’t have a Sanhedrin, etc.” is very problematic in my opinion. It is unlikely that a stage will come when the entire people of Israel will understand that it is moral to act this way and will accept these things. This is completely delusional and I think the rabbi would agree with me about this plausible prediction. If so, then the fact that perhaps the halakha will prevail is just a theoretical statement that will probably not have any meaning in the future either… Maybe a fundamental change in halakha is needed? One that does not directly conflict with morality?
Thank you very much.