The authority at the top of the chain of command in a deployment isn't just a matter of theory. In this case, there's a specific mission being executed under the authority of the CinC. We're not talking about routine, day-to-day procedures or training exercises or military minutia. Lakin isn't questioning the authority of those who are immediately above him and convening the court martial, but the "One" who is above them and has set the strategic objectives they are working to fulfill. Does the president have immediate authority over the execution of a military objective in Afghanistan (where Lakin was ultimately to be deployed). That answer is yes.
I doubt the court martial will agree.
Probably not. It seems that such bodies tend to avoid the big picture, but they do so in this case at the expense of our military's and nation's integrity.
Also, They may convict Mr. Lakin but they then open themselves up to critical review in the future if Obama is forced to reveal that he represented himself as a Kenyan when he was an adult in another case.
These men can deny his right to discovery and then convict Mr. Lakin, but they deny discovery at their own peril.