No, a command is generally not permitted to initiate or process an administrative separation for a service member while there are ongoing court-martial proceedings against them for the same underlying conduct. The military justice system gives precedence to the court-martial process. A court-martial is a federal criminal trial with the highest level of procedural protections and the most severe potential punishments, including a punitive discharge. The administrative separation process, with its lower standard of proof, must wait.
The rationale for this rule is to prevent administrative processes from interfering with or improperly influencing the criminal trial. The service member and their defense counsel must be able to focus entirely on defending against the criminal charges. Furthermore, the outcome of the court-martial will often dictate the administrative outcome. A conviction at a court-martial that includes a punitive discharge makes a separate administrative separation unnecessary. An acquittal at a court-martial significantly weakens the basis for any subsequent administrative action.
A military defense attorney would immediately object if a command attempted to initiate a separation board while court-martial charges were pending. The attorney would file a motion with the command’s legal office to have the administrative action placed on hold or “abated” pending the final resolution of the court-martial. This ensures that the criminal justice process is allowed to run its course without interference and that the soldier is not forced to fight a legal battle on two fronts at once.