In those trials, the court ruled the religious exemption can be over ruled by military need. You must remember the two parts of the ORIGINAL Constitution with the broadest authority given to Congress is in regards to interstate commence AND military needs. If you can avoid those two issues, the Bill of Rights come into full play. Thus look at Article I, Section 8 of the US Constitution.
Section. 8.
The Congress shall have Power To lay and collect Taxes, Duties, Imposts and Excises, to pay the Debts and provide for the common Defence and general Welfare of the United States; but all Duties, Imposts and Excises shall be uniform throughout the United States;
To borrow Money on the credit of the United States;
To regulate Commerce with foreign Nations, and among the several States, and with the Indian Tribes;
To establish an uniform Rule of Naturalization, and uniform Laws on the subject of Bankruptcies throughout the United States;
To coin Money, regulate the Value thereof, and of foreign Coin, and fix the Standard of Weights and Measures;
To provide for the Punishment of counterfeiting the Securities and current Coin of the United States;
To establish Post Offices and post Roads;
To promote the Progress of Science and useful Arts, by securing for limited Times to Authors and Inventors the exclusive Right to their respective Writings and Discoveries;
To constitute Tribunals inferior to the supreme Court;
To define and punish Piracies and Felonies committed on the high Seas, and Offences against the Law of Nations;
To declare War, grant Letters of Marque and Reprisal, and make Rules concerning Captures on Land and Water;
To raise and support Armies, but no Appropriation of Money to that Use shall be for a longer Term than two Years;
To provide and maintain a Navy;
To make Rules for the Government and Regulation of the land and naval Forces;
To provide for calling forth the Militia to execute the Laws of the Union, suppress Insurrections and repel Invasions;
To provide for organizing, arming, and disciplining, the Militia, and for governing such Part of them as may be employed in the Service of the United States, reserving to the States respectively, the Appointment of the Officers, and the Authority of training the Militia according to the discipline prescribed by Congress;
To exercise exclusive Legislation in all Cases whatsoever, over such District (not exceeding ten Miles square) as may, by Cession of particular States, and the Acceptance of Congress, become the Seat of the Government of the United States, and to exercise like Authority over all Places purchased by the Consent of the Legislature of the State in which the Same shall be, for the Erection of Forts, Magazines, Arsenals, dock-Yards, and other needful Buildings;—And
To make all Laws which shall be necessary and proper for carrying into Execution the foregoing Powers, and all other Powers vested by this Constitution in the Government of the United States, or in any Department or Officer thereof.
Notice the language in regard to the Militia, it is very broad and that has been viewed as including who is a member of the Militia. By US Law, all males between the ages of 18 and 45 are members of the "Reserve Militia" UNLESS on Active Duty OR a member of the National Guard (There are a few other exceptions, all minor, and a reference that women serving in the Guard are also members of the Militia). Thus Congress can call up anyone to serve at any time. The First Amendment has NEVER been viewed as creating an exception to that rule.
Now, in the Civil War, it was possible for Citizens who did not want to be drafted to buy they way out. In many ways the Draft of 1863 was designed to create a pool of people who would gladly pay veterans, whose enlistment had ended, to reenlist as a substitutes. By 1863 all the money for enlistment bonuses had dried up and the draft was designed to get people to come up with the money to encourage such reenlistment. Some historians question if anyone was really drafted in the 1863 Draft for even in New York City, which had Draft Riots against the Draft, ended up setting up funds to pay for such substitutes for people who could not pay the the substitute themselves.
WWI had no exception for Religious reasons. Now individual Officers could rule a man was unfit for duty do to his religious objections but only after that person had been assigned to a unit being sent to the Front (and most officers new they needed every man they had so rarely done).
For WWII, a religious exception was created, but it is viewed as a product of legislation NOT the Bill of Rights. As written it only included those people who were members of a religion that had a CLEAR objection to going to war. Objections to a particular war was NOT enough, objection to being shot out was NOT enough. You had to meet the STATUTORY requirements of the law. Efforts to expand those exceptions failed during WWII and Vietnam, with the courts deferring to Congress in that matter.
Just a comment, when it comes to the draft you have to look at the Militia clauses and those clauses have NO exemptions to them.
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