If the constitution provides that we will "make no law prohibiting the free exercise" of a citizen-soldier's religion, then we must permit that religion to be fully practiced AND THIS ESPECIALLY SO if we're putting the life of the soldier in jeopardy. At such a time, a person would DEMAND access to his full religion. A full expression of religion requires the presence of ministers of that religious faith.
Since commanders historically control access to their soldiers, preventing most media, spectators, life insurance salesmen, etc. from seeing them prior to battle....for obvious reasons....then commanders must decide if they want non-affiliated religious leaders to have access to their troops or if they want affiliated religious leaders to have access to their troops.
Commanders have chosen that religious leaders ministering to their troops at time of battle have some relationship to the command structure. First, commanders recognize that when death is imminent, relgious leaders become extremely powerful in the lives of human beings. Second, commanders realize that full expression of religious faith is a Constitutional right. Third, commanders recognize that death-frightened men will FIND religious leaders whether the command provides them or not.
For legal and practical reasons that relate to the men AND to the control of the "religous leader/chaplain" a wise commander will want that religious leader on his staff and subject to his direction.