The military culture in the United States hides sexual assault cases many times. Because of this, sexual assault cases should be removed from the military's chain of command and from the military's own judicial system. A sexual assault is illegal in all 50 states, so members of the military should be prosecuted to the fullest extent of the law outside of their employer.
These commanding officers have obviously not done a good job, so they should not be trusted to investigate themselves. Its basically an appeal to ignorance, "I didn't know what I didn't know. But I wasn't supposed to know it, so its ok that I didn't stop this."
Part of a REAL investigation of rape is environmental - HOW did this happen, not just WHO did it. HOW these things happen is failure in discipline that is traceable to the Command.