In the midst of World War II, some schoolchildren refused to salute and pledge allegiance to the American flag for religious reasons. In spite of pleas that state laws requiring these practices were necessary to promote national unity, the United States Supreme Court ruled in 1943 that the First Amendment demanded an exemption for these students. America was still able to win the war.The short piece mainly argues for such accommodations on policy as opposed to constitutional grounds and that is good because whether the First Amendment's Free Exercise clause, properly understood, guarantees such is a complicated matter contested on grounds that transcend politics. Legal scholars on the Left and Right fall on both sides of this question.
During Prohibition, religious Americans were permitted to use wine for sacramental purposes. Today, Native Americans are allowed to use the narcotic peyote in religious ceremonies. The abuse of alcohol and drugs has caused great harm, but few would attribute this damage to these accommodations.
In Wisconsin v. Yoder (1972), the Supreme Court famously ruled that Amish families could not be forced to violate their religious convictions by sending their children to public schools. Quakers and others are permitted to affirm rather than swear oaths, in spite of concerns that allowing them to do so poses a risk to the integrity of the judicial system.
Justice Scalia, Philip Hamburger and Marci Hamilton on the one side (that the Free Exercise Clause doesn't guarantee such accommodations) v. Justice O'Connor, Douglas Laycock and Michael McConnell on the other (that the FEC does).
I endorse the notion in Smith that the FEC clause does NOT guarantee such accommodations on constitutional grounds. But on policy grounds (statutes, etc.), I support such. Likewise as a libertarian I believe every consenting adult should be able to do peyote regardless of the motivation behind the action.