Why not throw in 85 as well?
(Not that I know my UCMJ, I googled it :) )
I think the reason that the Army went with Missing Movement rather than desertion is the first stipulation in Art. 85. It says the person must leave his post, etc., with the purpose of remaining away permanently. Watada never went missing, he just refused to get on the bus to the airfield to deploy.
Usually desertion is a charge saved for those who have gone UA, Art. 86 for a specified period of time. Desertion would include guys that run to Canada to avoid deployment to a combat zone.
I know we all want to see this guy fried for everything, but we also need to look at it from a big Army perspective. They want to get this over with quick with the three charges that will be quick to convict. Enough prison time to set an example, but get it out of the press quickly.