There is a mitzvah deoraita (Biblical commandment) to bury a person executed by bet din (Jewish court of law). Similarly, there is the law that a righteous person should not be buried next to a wicked one, derived (Sanhedrin 47a) from the story of Elisha Hanavi in Sefer Melachim (II 13:21).
The Gemara in Yevamot 32a discusses the definition of tzadik (righteous person) and rasha (wicked person) with regard to these laws and concludes that those who committed multiple severe offences (e.g. Eishet Ach and Achot Ishah) which give them the status of rasha gamur (completely wicked person) should be buried in the grave-yard where they bury those who died at the hand of Beis Din by serefa and skila (such as one who was mechalel shabat) and not in the graveyard of "not-so-wicked" (Rashi) people who committed capital offences warranting chenek or hereg (such as murder).
Why is mechalel shabbat considered such a thoroughly wicked act? It would make more sense that other deeds such as murder are more wicked.
(I realize that symbolically, chilul shabbat is compared to things like idolatry, but so is getting angry. It's hard to hear that one who picks the chicken bone from the meat on Shabbos (violating borer, sorting) should be considered more wicked than a murderer.)