* Where the preamble declares, that coercion is a departure from the plan of the holy author of our religion, an amendment was proposed by inserting "Jesus Christ," so that it would read "A departure from the plan of Jesus Christ, the holy author of our religion;" the insertion was rejected by the great majority, in proof that they meant to comprehend, within the mantle of its protection, the Jew and the Gentile, the Christian and Mohammedan, the Hindoo and Infidel of every denomination.
-Thomas Jefferson, Autobiography, in reference to the Virginia Act for Religious Freedom (from which the 1st amendment is derived)
The relationship between Native American Tribes and the US government is a bit more complicated than you are indicating here. Native American Tribes are afforded an extra degree of sovereignty and authority, and are actually recognized as "domestic dependent nations". This is where the exemptions for their religious ceremonies come from.
From wikipedia:
"Congress passed an amendment to the American Indian Religious Freedom Act of 1978 (42 U.S.C. § 1996), i.e., the American Indian Religious Freedom Act Amendments of 1994 (42 U.S.C. § 1996a), pertinent excerpts of which are given below: Use, possession, or transportation of peyote Notwithstanding any other provision of law, the use, possession, or transportation of peyote by an Indian for bona fide traditional ceremonial purposes in connection with the practice of a traditional Indian religion is lawful, and shall not be prohibited by the United States or any State. No Indian shall be penalized or discriminated against on the basis of such use, possession or transportation, including, but not limited to, denial of otherwise applicable benefits under public assistance programs. —42 U.S.C. 1996A(b)(1)."
Note that "bona fide" and "traditional" language.
You are probably going to ask who decides if use of peyote is actually protected under this act or not. The answer seems to be a jury of one's peers. Laws are often written to provide guidance for how one's actions should be judged, and do not provide a detailed "if-then" case for their application.
Whether or not peyote should just be fully legalized across the country is a different question.
Recognition of your religion would likely be determined at the time of your trial.
Should that be the courts right? I would argue no.
Sources: http://www.irs.gov/irm/part7/irm_07-025-003.html#d0e1146 http://en.wikipedia.org/wiki/Establishment_Clause
I'm going off a few quick searches, but the peyote bit seems to exclude it for any "bona fide ceremonies" for the Native American Church, regardless of race. I didn't see any mention that they must be on reservations either. Wikipedia also notes that some states have a "bona fide religious" exemption that's not related to the NAC (which is at least somewhat more consistent, but "bona fide" is still silly to apply in this scope).
I don't understand the full ramifications of the treaty and legal status myself. My point was just to indicate that the flippant remark about "some religions can use peyote" leaves out a lot of historical, political, and legal context.
That's the point of the Supreme Court, which did it's job and confirmed that the government is not supposed to determine what constitutes a religion.
The Sikh kirpan (knife) issue hasn't been argued before the supreme court. When it is, I expect a school's right to ban that weapon will be affirmed on the same grounds.
There are other exemptions too for religion, where they decide what a real religion is. I think, for instance, conscientious objectors needed to have an approved religion.
(There should be no freedom of religion explicitly; it just opens things up for abuse and silly interpretations. Freedom of speech, thought, assembly and so on should be more than enough to include religion.)