One axiom that has been with the military as far back as history can be studied: when one is absorbed by a military - voluntarily or through conscription - he forfeits his rights (whatever they may be within his particular culture) and gets them back selectively, as privileges.
My guess is that the forced-religion charge was brought as a method of circumventing his willful obligation to serve (getting an honorable discharge - maybe with a cash settlement). Beats going AWOL or deserting. The court’s inconsistencies, however, leaves the outcome of this stupidity rather blurred.