The United States government has absolutely no right to hire chaplains from any denomination or religion for the military or any other area of our government. If a believer joins the military and is blessed to witness or minister to other believers, they cannot be stopped. However, tax dollars should never be used to establish, support, or promote any religion or religious activity.
As for the prohibitions regarding prayer, no man can prohibit true prayer at any time, as it is the Spirit that makes intercessions with groanings that cannot be uttered!
I agree with James Madison on this issue. See “Detached Memoranda”
“Is the appointment of Chaplains to the two Houses of Congress consistent with the Constitution, and with the pure principle of religious freedom?
In strictness the answer on both points must be in the negative. The Constitution of the U. S. forbids everything like an establishment of a national religion. The law appointing Chaplains establishes a religious worship for the national representatives, to be performed by Ministers of religion, elected by a majority of them; and these are to be paid out of the national taxes. Does not this involve the principle of a national establishment, applicable to a provision for a religious worship for the Constituent as well as of the representative Body, approved by the majority, and conducted by Ministers of religion paid by the entire nation.
The establishment of the chaplainship to Congs is a palpable violation of equal rights, as well as of Constitutional principles: The tenets of the chaplains elected [by the majority] shut the door of worship agst the members whose creeds & consciences forbid a participation in that of the majority. To say nothing of other sects, this is the case with that of Roman Catholics & Quakers who have always had members in one or both of the Legislative branches. Could a Catholic clergyman ever hope to be appointed a Chaplain? To say that his religious principles are obnoxious or that his sect is small, is to lift the evil at once and exhibit in its naked deformity the doctrine that religious truth is to be tested by numbers. or that the major sects have a right to govern the minor.”
Is this not also true of the military chaplaincy?
I don't know how to work it out, because I, too, can see he perilous disadvantage in the gvt. directly paying salaries for chaplains. In times past, it was not such a salient problem. But now it's a big one, because the chaplain has to represent Christ's Church: not Holy Mother the State.