I get VERY clinical with things like this and suicidal ideations. Have a process or a battle-drill beforehand, something, and then practice it. When you’re done, put it in a drawer, pull it out every couple of months and practice it some more.  You have to KNOW how to react when it happens, before it happens. Because when it happens a lot of things happen quickly, things that have life/career ending/destroying consequences.

For leaders. In today’s environment, the first thing I would say is raise the flag. If you’re a company commander (especially if you’re a PL!!!) there is no reason to keep a report of sexual assault at your level.
If the victim is in your unit, take steps to ensure they are protected, receive the applicable tests and counseling is made available. Ensure there are not reprisals, intimidation, or anything else that prevents the victim from feeling safe. Consider companionate reassignment or short term attachment.
If the suspect is in your unit, they are still innocent until proven guilty. As a leader you need take steps to ensure they are protected as well. The rumor mill be the killer here; crush them when and where you find it. Ensure the suspect is aware of their rights, and have contacted representation.
If both are in the unit, ensure not to take sides. Follow the steps I mentioned above; have compassion for the victim and deal with the suspect professionally.  Obviously change their duties if they would typically come in contact with one another, even to the point of reassigning or attaching out one of them.
In the end, be prepared to drop the full weight and authority of the UCMJ on the suspect, OR the “victim” should it be found they were lying (I personally think we don’t prosecute enough Art. 107 violations).

With this story though, I think we have to take a step back and look at it with our presentism glasses off. Marine Corps, 2006; the military as a whole was still going through the strains and sprains of “don’t ask,” and there weren’t a more oo-rah group of “manly-man” individuals, than found in the Marines. There was an absolute stigma associated with male Marines getting assaulted by other male Marines. Being a man myself, I can understand it at a basic level. Is that right? No, but it’s reality and refusing to deal with reality does more harm than good.  
How as a leader would I prevent this sort of thing in my company today? Make it clear to your Soldiers that these things DO happen. Be the leader that gets up during SHARP and EEO training, looks them all in the eye, and tells them that “woman and men can be victims, one isn’t worse than the other. It can happen, and if it does my door is open.”  Sexual assault is wrong, abhorrent to our values, and needs to be punished as swiftly and brutally as military justice is able.