Confidentiality is one thing, but when a crime has allegedly been committed, that makes confidentiality less of a valid issue. Kramer moving up in the leadership could have given him more authority to commit crime unchecked, as more authority can equal the ability to shut people up. When Kramer moved up, that's when Johnson should have had a talk with the leadership.
I'd argue that he should've made that appeal to the alleged victim first. If, after making that plea, she still wanted him to stay quiet, I still think there's an ethical problem with violating her wishes.
Well, that's one opinion, which you are entitled to. Personally, I think that sexual assault is a serious crime, and if someone is alleging it, the proper authorities should be notified, regardless of rather or not confidentiality is requested, because other persons could be at risk of being attacked.