I think it helps to think about how a comparable situation would be received in other contexts. Yes, the military, in how it administers justice to its members, has some inherent differences. For one thing, your civilian boss can't, in most cases, have you locked up for disobeying his or her directives. However, deciding whether an individual should be prosecuted and at what level, when the alleged offense is a serious crime against another Service Member, should be the call of a legal professional - one not personally involved with what may be the internal politics and machinations of a military command. Again I'll ask the question: If your wife, daughter or sister were raped by a co-worker, would you want their boss to decide whether to prosecute the alleged offender?