And what penalty did his superiors receive? Nothing. Privates should never have access to secret information without supervision. If he did someone else should be responsible and take the penalty.
If you paid attention to the sentencing hearings, it was clear that the chain of command should be largely responsible for the happenings of the Manning case. They repeatedly ignored and swept under the rug issues related to his mental state and fitness for duty, and a lot of it was done for the reasons of DADT.
The US military has subtle mechanisms that would not be obvious externally. I'm sure it varies and changes, but something as simple as the timing of an officer's promotion, or review without promotion, can signal an "end of career" event. Someone familiar with the branch and with access to the promotion data could tell you if an officer in the chain may have been held responsible.