You are missing something: military lawyers on the prosecution side are like any other prosecutors: they have prosecutorial discretion. In other words, they can essentially say “this case stinks, we are not going to prosecute.” (The story is a little different for defense lawyers. Won’t get into that here.)
BINGO. Let me tell you a short story just about just that. When I was chief of military justice at an USAF base in TX many years ago, we prosecuted a senior NCO who shipped back a lot of military equipment from his unit that he had been deployed to in the Desert. Stuff like a few dozen multiplier tools, bayonets and the like, nothing huge. It got flagged by customs.
His story was that the unit in the Gulf had more of this stuff than it could ever use, but his police unit stateside was woefully short on them and having trouble getting the stuff, so he was shipping it back with the intent to give out to members of his unit at our base. (He was a supply NCO among other things at that unit).
Of course it sounded self-serving, and of course he had no evidence to corroborate the story. We preferred court-martial charges.
As his case got ready for trial, word finally started getting around his security police community about his trial. Then, literally a couple of days before trial, two other police troops from a different base contacted us. They had been deployed with him, and they remembered conversations with him out there on more than one occasion when he told them that he was going to send some of these "excess supplies" back to his home unit.
Well, this was a year later, he had forgotten the conversatiosn himself by the time the whole thing came to light, so he had never given us their names.
Now - to be clear - he did NOT have authority to ship these supplies back to his home unit. But these 'out of the blue' alibi witnesses basically blew our intent to steal element out of the water.
Instead of going through with the trial (we could have gotten him on a lesser charge even if these witnesses were believed), my Staff Judge Advocate and I went to the 2-star Convening Authority and asked him to dismiss the charges, because had we heard these witnesses before the process got started, we would never have recommended a court-martial be convened (he might have gotten a Letter of Reprimand or less).
The easy way would have been to just go through with it, and risk saddling an otherwise spotless 20-year NCO with a federal conviction.
The RIGHT thing to do was was to make sure it was as if it "never happened".
The general dismissed the charges as we recommended, and I personally apologized to the NCO about the putting him through the whole thing - on my own initiative - because he had served in the first Gulf War and had a spotless record.
THAT story is my example of how the military justice system, when followed, is MORE just than its civilian counterpart.
That is the 'other side of the story', but like all such stories, the final outcome in such an unclear case will largely depend on the character of the officers involved. My 0-6 boss SJA was highly attuned to justice and had no need of convincing to do the right thing.
Sadly, I can't say that about every senior JAG officer I worked with.