In 1998, the Clinton Administration authored a change to the Manual for Courts-Martial, which provided that cases of adultery be handled at the lowest appropriate level, and provided specific guidance for commanders to use in order to determine whether or not the member's conduct was "prejudicial to good order and discipline," or "of a nature to bring discredit upon the armed forces." While the President does have the authority to issue changes to the MCM, this proposal resulted in screams and yells from Congress, and was subsequently dropped.
However, in a very quiet move, in 2002, President Bush adopted many of the changes that were proposed by President Clinton. In addition to the Elements of Proof," the "Explaination" section under this offense now requires commanders to consider the following factors when determining whether or not the offense of "adultery" constitutes a crime:

The accused's marital status, military rank, grade, or position;

The co-actor's marital status, military rank, grade, and position, or relationship to the armed forces;

The military status of the accused's spouse or the spouse of co-actor, or their relationship to the armed forces;

The impact, if any, of the adulterous relationship on the ability of the accused, the co-actor, or the spouse of either to perform their duties in support of the armed forces;

The misuse, if any, of government time and resources to facilitate the commission of the conduct;

Whether the conduct persisted despite counseling or orders to desist; the flagrancy of the conduct, such as whether any notoriety ensued; and whether the adulterous act was accompanied by other violations of the UCMJ;

The negative impact of the conduct on the units or organizations of the accused, the co-actor or the spouse of either of them, such as a detrimental effect on unit or organization morale, teamwork, and efficiency;

Whether the accused or co-actor was legally separated; and

Whether the adulterous misconduct involves an ongoing or recent relationship or is remote in time.