So called "acquaintance rape" (or "date rape") cases are very difficult.
Essentially, boiling this down and simplifying it a great deal, under our sexual assault laws a male or female must give consent for lawful sexual intercourse. (Generally we are dealing with women so I'll use those pronouns, etc.) If a woman is heavily intoxicated, she could either be unconscious (and therefore incapable of giving consent), or semi-conscious but incapable of giving consent because of a lack of ability to have the coherence of thought necessary to give consent. So, to over-simplify, if someone is drunk and their eyes are open, it does not automatically mean they can give consent in a legal sense.
If the person initiating the sexual intercourse (let's say it is the man) is heavily intoxicated but can function enough to perform the sexual acts, there is a presumption that the initiator is conscious and legally responsible for the person's actions. (Heavy intoxication could potentially be a mitigating factor in the sentencing phase in terms of showing impaired judgment). Theoretically, someone could argue that they were able to initiate sexual intercourse without being conscious in a legal sense. By way of analogy, in first year criminal law courses you read cases where people who were sleepwalking killed someone, acting out a dream (famous case in England where a mother killed grown daughter with axe while sleepwalking, dreaming that she was hitting an attacker on top of daughter). However, the presumption is, again, that someone able to perform relatively involved physical actions was also conscious enough to have intent within the meaning of the criminal law.
These acquaintance rape cases are VERY, VERY difficult to prove. Sometimes close to impossible, because unless there is third party testimony (that someone assaulted a comatose/passed out individual), the alleged victim's testimony is often not enough -- because almost by definition the victim could not observe/think/remember if the issue is one where the victim was incapable of giving consent because of incapacitation by alcohol.
From what I have read about this case, the authorities could not develop the third party evidence they needed. That in itself is no fault of the authorities -- if it's not there, it's not there -- but it sounds like they may have also made a serious procedural misstep in the investigation and lost evidence from one of the allegedly involved midshipmen because of a failure to read him his rights. However, the acquittal is not necessarily a vindication in the sense we might think as laypeople -- an entirely appropriate acquittal for failure to meet the very high burden of proof of "beyond a reasonable doubt" does not mean that the alleged victim was lying, for example -- it may just mean a lack of evidence. Of course, it could also mean the assault did not happen at all -- there is a wide range of possibility. Think the OJ case -- one jury found him not guilty of murder under the "reasonable doubt" criminal standard, and a later jury found that he killed two people using the "preponderance of the evidence" (more likely than not) non-criminal standard in the wrongful death civil case for damages.
As I understand it, the defendant has agreed to resign from USNA rather than be subject to a conduct investigation at USNA based on the finding of the trial judge that he lied in the course of the investigation. So, to analogize to civilian criminal practice, it would be like going after a defendant for lying to the FBI even if he was found not guilty on the underlying offense. (The "Scooter Libby"/Valerie Plame case was a case like that -- in leaking Plame's name to the press Libby did not actually violate federal law, but it was alleged and a jury found that he subsequently lied to federal investigators about his actions, and the lie was the crime for which he was prosecuted.) Rather than subject this midshipman to another naval criminal proceeding, they made a deal that he'd resign through USNA channels rather than contest the issue of lying in the course of the investigation.
I don't know enough about the case to know what they would charge the alleged victim with in terms of conduct. If she was underage, and they charged her, questions would be raised about whether the Academy goes after all those who drink off campus while underage. Obviously you would also have the issue that someone who was an alleged victim of sexual assault involving alcohol consumption would be dissuaded from reporting the assault for fear of punishment for the alcohol. This was the case in prior years at the Academies and they took significant criticism for this from Congress, the media, the public, and legal experts.
As others, including NavyHoops, have pointed out, excessive alcohol consumption (especially by young people) leads to some very ugly problems/incidents, as anyone who has ever been responsible for young soldiers/sailors/Marines -- or been to college themselves -- knows. There's an interesting article in the Atlantic about alcohol related deaths and subsequent litigation at college fraternities that illustrates the same point and shows it goes far beyond the military or service academies.
