Sounds like the judge is incapable of stopping the trial from degenerating into a left wing Bush hatefest.
If he doesn't want to go to Iraq send his butt to Afganistan.
If a new trial were to go forth, the two dropped charges plus the charge for failure to obey a lawful order would be charged against him. Such would add to his punishment if convicted.
Watata is guilty or not guilty - his reasons for disobeying orders and missing shipment are immaterial.
If he is found guilty, that testimony may be introduced along with other matters of extenuation and mitigation. Following the defendent's presentation of matters of extenuation and mitigation, each member of the court will enter a recommended sentence on a slip of paper which will be placed in a hat. The proposed sentences are drawn from the hat and sorted by severity; the court then begins to vote on each proposed penalty beginning with the least severe - the first proposed sentence that receives a majority vote is adopted.
So, the judge declares a mistrial and Watada gets a new judge and is court-martialed on two additional charges. Apart from a little lost time, what's the downside?