Aside from a presidential pardon if the man is convicted, there isn’t anything Obama can do to rescue him from the path he’s chosen.
There are a lot of steps between a Court Martial and a Presidential Pardon. They are called appeals. The first one might even be automatic, depending on the sentence imposed. The Court has the option of pretty everything from essentially nothing, up to but not including death, unless the offense is committed "during wartime", then even death is an option.
The Missing movement charge only allows a maximum of:
Dishonorable discharge, forfeiture of all pay and allowances, and confinement for 2 years.
They aren't going to give him anything terribly much for failing to report, under the circumstances. (essentially an administrative, as opposed to operational, order).