Most of the major villains in the show did a lot of truly awful things in their lives. For Zelena, her deception of Robin Hood was among those things. However, in the grand scheme of everything awful she ever did, it's one of the lesser on the list. Zelena likely killed, cursed, transformed, terrorized or otherwise ruined the lives of dozens of people in Oz, The Enchanted Forest, and briefly Storybrooke when she was The Wicked Witch of the West. Most of those are just assumed statistics, which tend not to stick as much as detailed individual accounts of wrongdoing, such as murdering Marian, stealing her identity, and inducing Robin into companionship, sex, and production of a child, or tricking Neal into his own death.
The show's general position on punishment of villains for their past deeds is that if non-intentionally-fatal punishment is meted out by heroes while the villain is still villainous, it's generally righteous. However, if a villain starts down the road to redemption, then a villain can, in time, effectively earn forgiveness. This isn't generally how it goes in our world, because for the most part, we rightly don't trust that very bad people can be redeemed. However, the show involves magic and has an objective means of determining where a story realm character sits on the villain-to-hero spectrum, which is the darkness or lack thereof in one's heart. This is a changeable condition based on conscious choices, and it changes the character of a person. From a certain point of view, it might raise the question, if a former villain is now objectively and truly a good person or a hero, with potential for good or heroic deeds going forward, then aside from ordering and enforcing restitution (if feasible), what greater purpose is served by punishing this good person or hero for past misdeeds that person now deeply regrets? Additionally, any time punishment is considered in our criminal justice system, a judge will consider not only the facts of the offense, but also any matters in aggravation (including prior criminal background or misdeeds) and any matters in mitigation (such as contrition, cooperation, undue hardship, etc.). In Zelena's case, after Robin Hood's death, she was a single mother to baby Robin, who she truly loved (granted, Zelena's misplaced trust of Hades contributed to the cause of Robin Hood's death). Despite Zelena's past, she could become and did become a fit mother. By the time season 6 ended and Zelena had realized the poor choice of choosing to align herself with The Evil Queen over Regina, she was probably over the villain hump, but still a bit snobbish and given to the occasional whiny fit of self-pity. However, by the end of season 7, after the Kelly-ification of Drizella's dark curse, Zelena was probably a solid hero. One additional thought: I don't think the show suggests that Zelena became a better person by raping someone. Zelena became a better person after her deception of Robin Hood, but the show doesn't suggest that it was because of it.