Morals and Halacha

Hello Rabbi, as I understood from the Rabbi, in many places the Rabbi distinguishes between morality and halacha, and the moment the two conflict, the Rabbi claims that in unique cases morality will prevail over halacha (i.e., saving a Gentile on Shabbat).
I wanted to ask how the rabbi behaves like this? After all, the sages knew that it was immoral to let a gentile be killed on Shabbat, and yet they said that it was forbidden to save him, so how is it that the moment the rabbi chooses to save the gentile, it is not the same as any ordinary person who, due to a certain difficulty, chooses not to observe the halacha?