Hitman has always been an edgy video game series, from its serious themes to its calculating gameplay where you kill various people. Murder in the first degree was not the real reason a magazine advertisement for Hitman Blood Money attracted controversy in 2006; the ad mixed sexuality and violence to a degree that made some uncomfortable.
In the U.S., a degree of violence is tolerated in many mediums but when sex enters the equation all bets are off. The fact that a woman is killed in the photo is almost immaterial; her short, revealing gown combined with an obvious bullet wound in her forehead made many think this scene depicted two crimes – rape and murder. The fact that Hitman protagonist Agent 47 would never rape a woman doesn't really matter: the image spread around the Internet and caused a typhoon in a teacup.
Despite the Hitman series being one of the closest depictions to a "murder simulator" out there, this was one of the most controversial moments in the series' history along with the depiction of Sikhs in Hitman 2: Silent Assassin. Speaking to Eidos, we know the perceived malicious intent wasn't intentional and there were no real long term effects to the franchise.