At the Volokh Conspiracy,  Stuart Benjamin raises an important question, asking:

whether we can articulate any useful metrics for when we should defer to self-serving statements by those with access to more information, and when we should not. In the two instances above, the doubters were vindicated. There are other examples in this vein. LBJ had access to greater information about the Gulf of Tonkin incident than did the doubters, but the latter were right, as the Pentagon and LBJ misrepresented what happened…

But there are counter-examples. Many people believed that Julius Rosenberg was innocent, but it is now clear the government really did have the goods on him, and that he was guilty. Same for Alger Hiss. Indeed, the airstrikes that President Clinton ordered at the height of the Lewinsky imbroglio – which were widely criticized as trumped up attempts at diverting attention, with little deference to the information asymmetry favoring the President – look quite different after September 11, 2001.

Two strategies for dealing with such asymmetries come to mind. One is an ex ante strategy, working to place unusually trustworthy individuals and groups in such positions (life-tenured judges, bipartisan committees, etc) or in positions where they can provide credible signals about justification (as Auditor-General, for instance). The other relies on the shadow of ex post punishment, which could be increased in inverse proportion to the probability of eventual detection.