I totally agree it has been misinterpreted, I'm pretty sure the intention of Jefferson and Madison was that the government is not supposed to be able to determine what constitutes a religion in addition the right to believe & practice it* . The inclusion of the word "religion" seems a practical response to the tendency of governments to ban practices that threatened their power.
* 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)
Doesn't "we can't interfere with a religious practice" plus "we can't determine what is a legitimate religious practice" mean anyone can claim anything to be a religious practice? "Oh, I'm sorry, I'm engaged in the blessed sacrament of the mugging."
This is where it's worth remembering that humans are in the justice system by design. While the line is intrinsically fuzzy, one can at least agree that at one extreme a marijuana user coming up for charges who suddenly claims he has a marijuana-based religion in an attempt to get out of it isn't going to get very far. Judges are not required to be as stupid as computers interpreting the law.
On the one hand, judges are still part of the government. On the other, the first amendment says "Congress shall make no law regarding the establishment of religion", not that "judges shall make no rulings".
* 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)