A couple things here. The military doesn’t throw O-6s in pretrial confinement on “he-said/she-said” evidence. This is probably related to his AWOL and he’s therefore a potential flight risk. It also speaks volumes about how strong the evidence is. Why would he be a flight risk if the evidence is flimsy to nonexistent?
And officers who are facing these sorts of charges ALWAYS fight hard at the Article 32 level to try to make the waters murky enough to get command to opt for a RILO (resignation in lieu of) court-martial. His not opting for that fight also speaks volumes.