Answer

The punishment does not necessarily indicate the severity of the offense. Apparently the medieval authorities (Rishonim) disagreed about this (Sefer Hasidim and Maimonides). Maimonides also writes in the Guide for the Perplexed that there are four reasons to make a punishment more severe, and only one of them is the severity of the offense. See, for example, a short article from last Sabbath:
I wrote a long article about this years ago: The Theory of Halakhic Punishment.
——————————————————————————————
Questioner:
If so, then I wanted to understand why the Sabbath really is more severe than Yom Kippur, if the severity of the punishment does not indicate the severity of the act?
——————————————————————————————
Rabbi:
My statement was a matter of principle, but regarding the issue itself I can try to suggest an explanation. For example, desecrating the Sabbath is perceived as a denial of creation and of the Creator. Yom Kippur is an important commandment, but it is not essential to the very service of God. Therefore, one who publicly violates the Sabbath is like one who rejects the entire Torah.
——————————————————————————————
Questioner:
It is brought in the name of the Chafetz Chaim that at the end of the Torah portion of Acharei Mot he cites two verses: one about the prohibition punishable by karet for one who has relations with his sister, and the other about the prohibition punishable by karet for one who has relations with his wife while she is a niddah. The Chafetz Chaim says that from these two verses you can see how problematic the outlook of the masses is, and how far it is from the Torah’s outlook. After all, in the public eye, if someone were caught having relations with his sister, he would be condemned, distanced, and become utterly repulsive to the public. But if someone were caught having relations with his wife while she was a niddah, the attitude toward him would be much more forgiving—that is, they would still condemn him, but much less so, and they would forgive him much more quickly—and the Chafetz Chaim says that this is incorrect, because the Torah punished both of them with exactly the same punishment—karet—which implies that they are equally abhorrent, and anyone who does not relate to it that way is an ignoramus. I wanted to ask what you think, because I do think I would relate to them differently; for example, I would treat someone who had relations with another man’s wife more severely than someone who had relations with his wife while she was a niddah.
——————————————————————————————
Rabbi:
I do not agree with him. First, the severity of the punishment does not indicate the severity of the offense. Second, there is a difference between moral severity and halakhic severity. Even if the punishment does indicate the severity of the offense, that is halakhic severity and not necessarily moral severity.