<disclaimer: I did not read the entire thread>
Having been a guy that had to deal with this from a leadership standpoint... I personally feel that the military chain of command involvement in a crime investigation that happens off post, in the US, and is covered by civilian law, is out of place in the 21st century. I have seen it first hand that this was the case. But, not always.
On post, in another country, aboard ship, etc... Then the UCMJ and the Chain of Command should (and are) the only ones involved.