Melanie D. Wilson, Finding a Happy and Ethical Medium Between a Prosecutor Who Believes the Defendant Didn't Do It and the Boss Who Says That He Did, 103 Nw. U. L. Rev. Colloquy 65 (2008).
The trial counsel (prosecutor)[n.1] works for the SJA, the SJA works for and advises the convening authority, the convening authority decides what cases go to trial and how they might be desposed of. I'd like to see the trial counsel try this recommendation.
As trained advocates with no personal stake in the outcome of a case, prosecutors are capable of presenting both views. During preliminary hearings, bail hearings, trials, sentencing hearings, and numerous other proceedings, the court routinely asks, "What's the government's position?" When a prosecutor disagrees with her supervisor about the government's position, what's wrong with telling the court that the "office's position is X but my own view is Y." For a concrete example, consider the prosecutor featured in The New York Times article.
See here for the ABA Standards for the Prosecution and Defense Functions. And here to read about the prosecutor who helped the defense.
[n.1] In the civilian community it is the defense counsel who is referred to as the "trial counsel."