Most of our daf focuses on the Talmudic rule of kim lei be-derabah minei – that is, a person who commits an act for which he is liable to receive two separate punishments, Jewish law will only allow him to be punished once, i.e. he will receive the more severe of the two punishments and be freed of the lesser punishment. Thus, if a person performs an act for which he would receive both capital punishments and lashes, he will not receive the lashes, as the capital punishment suffices as punishment for this act.
Our Gemara examines the opinion of Rabbi Nehunya ben HaKana who rules that Shabbat and Yom Kippur are the same with regard to this halakha. In other words, he believes that when a person commits a crime for which the punishment is karet (excision from the Jewish people) the rule of kim lei be-derabah minei will be invoked, and karet will be seen as the more severe punishment, even though karet is a punishment that is in the realm of the heavenly court.
According to Rabbi Nehunya ben HaKana, whenever there is a punishment of death for a given act, the Torah does not impose any other punishments on that person for having performed that act. Since karet includes mittah bi-yedei shamayim – a heavenly capital punishment – the same rule of kim lei be-derabah minei should apply. The Sages who disagree with Rabbi Nehunya ben HaKana argue that a court can only deal with issues that are within its purview, and it cannot take into account heavenly punishments. Moreover, as the Meiri points out, a sinner who is liable for karet has the opportunity to engage in a process of teshuva – repentance – and will be forgiven. Transgressions for which the penalty is capital punishment, the court will carry out the sentence, even as it hopes that the sinner will choose to do teshuva.