First, there is a thread currently out about this subject.
The issue at hand is participating in a public demonstration/protest/etc. while in military uniform when ordered not to by either the President or the chaplain's officers appointed over him.
The root of the problem goes deeper for Christians in the military than praying in uniform at a demonstration, but we have to win lesser battles before declaring the war's victory.
Bottom line, servicemembers follow orders given to them or they can expect to face administrative or judicial punishment. As an officer, the chaplain should either follow the order and fulfill his oath of office or resign his commission.
Cyril, Officer who takes neither Oath of Office nor Christian Faith lightly