Broadly counted every instance of rape, murder, and nudity in "Game of Thrones." An introduction to this data and methodology can be read here, along with the total numbers across all seasons.
Notable deaths: Roose Bolton, Balon Greyjoy, Olly, Alliser Thorne, Osha, Hodor, the Three-Eyed Raven, Rickon, Wun Wun, Ramsay, Lancel, Tommen, Walder Frey, Margaery, Loras, the High Sparrow
Notable rape scenes: None
This season has zero instances of onscreen rape (the first so far), perhaps a response to the backlash from Season 5. The plot lines of many strong women develop in an interesting direction here, precariously placing female characters into stations of "power"—only to shallowly tear half of them down in the next season.
In Season 6, Sansa escapes her rapist and helps Jon defeat the Bolton army, while her sister Arya trains to become a Faceless Man. These arcs both felt like victories, with Sansa coming into her own as a strategist and saving the day at the Battle of the Bastards, and Arya learning to become "no one" and re-shaping a foreign philosophy (aka Braavosi death cult) around her own ideals, needs, and moral compass. (Once they're reunited in Season 7, however, they're apparently unable to keep themselves from resorting to a childhood sibling rivalry.)
In King's Landing, the Faith Militant threatens commoners and noblemen alike, and we see two approaches to defeating the religious army with Cersei and Margaery. Clever, kind, and perceptive Margaery tries to manipulate the High Sparrow and his followers to accept her as a convert to their cause, signaling her duplicity to viewers by surreptitiously urging her grandmother to leave the city while she still can. Margaery's final gesture of atonement, however, is literally blown to bits by Cersei, who, following her highly sexual public humiliation by the High Sparrow, chooses to burn the Sept and everyone in it with wildfire. While Cersei is often pointed to as a "strong woman in power," her reign is built on acts of extreme evil, precarious alliances, and kingdoms in open rebellion.
Across the sea, Dany burns down all the Khals when they try to force her to retire from queenship.
Despite multiple female characters coming into power this season, only two episodes passed the Bechdel Test—both because of scenes with Arya. This season also had the most women's deaths, used to emphasize their murderers' previously-established ruthlessness (Osha and Lady Walda by Ramsay, Margaery by Cersei, background women citizens in Meereen by the Sons of the Harpy).