I agree with you. I believe that we as Christians have a responsbility to call on our God by name, to pray and read His word, obeying it. But unlike some in this thread, I do think that when a chaplain is paid by the state, the state has the right and responsibility to lay out the rules by which he goes about his job. If the state refuses to allow the chaplain to pray in the Name of Jesus, then I think what you're reading about God's warning to the Israelites has some relevancy. I personally believe that God has blessed this nation because we as a nation have called on Him. I also believe that we as a nation will lose that blessing if we neglect Him and disobey His commandments. The state who puts its Christian chaplains in this type of position, whether to obey the state or God, when he is called upon by the Bible to do both, is slowing reaping wrath upon itself.
From being in a military family for 20 years, I can say with much certainty that the military members do not have the same freedoms as civilians in relation to first amendment rights, etc. In that regard, it seems to me the chaplains will follow orders from command as military members first. What I am trying to say is that the military for them IS first; then the chaplain part of their service is second.
Many may disagree with this, but in relation to other areas of the military, I truly believe this to be the case in most if not all aspects.