The "evil" Pentagon and those nefarious bureaucrats that do nothing but clog up metro DC traffic have no role in this investigation. This is, for now, an internal matter for the 4th ID. The Commanding General, MG Ray Odierno, is the General Court-Martial convening authority.
The Division SJA made a recommendation to the Division Commander. Before we blame the JAG, we have a "commander's Army" believe it or not. The CG makes the ultimate call. The SJA only recommends based on a dispassionate legal analysis of the actions committed versus the law as written.
Additionally, for the SECDEF or Acting SECARMY to opine at this point in the investigation would be reckless and potentially exhibit illegal command influence. And POTUS has other things to monitor closely.
I would venture an educated guess that if LTC West is convicted, he will probably have his sentence set aside and be allowed to retire as a Major.