The Supreme Court’s decision in Lemon Versus Kurtzman was based on the Establishment Clause of the First Amendment. They decided that only legislation that could pass the Lemon Test was constitutional. The Lemon Test required that
The Supreme Court’s decision in Employment Division Versus Smith was based on the Free Exercise Law of the First Amendment. They decided that neutral laws of general applicability do not violate the Free Exercise Law. Since sacramental peyote use was prohibited, it was acceptable to deny unemployment benefits to persons discharged for such use.
One way in which other political institutions might limit the Supreme Court’s decision is to pass a constitutional amendment. Another way would be the executive branch simply not enforcing their decision.