In reality, they'll probably just get a slap on the wrist...maybe get an NJP and a stain on their record that will go away after a few years. They could also get dropped down in rank, and take a temporary pay cut. Court martial would probably only happen if the soldiers in question tried to get a lawyer to contest the charges. But if they're charged for disobeying a direct order from their general, (to not get pregnant/to not get someone pregnant on deployment) then there's probably not a whole lot that they can do to argue a case in court.
It's not like anyone's right to reproductive freedom is being suppressed. This is military life in a war zone. You knew you weren't supposed to get pregnant while you were out there, even though you could still have sex. Therefore, you should've used several methods of protection. Since you didn't, you disobeyed a direct order, and now others have to do your job while you go home/somewhere safe. Now you and your partner will be punished for disobeying a direct order. The letter of protest from Sen. Boxer and friends is just pure nonsense from people who have no clue whatsoever as to what is really going on.