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John Witte's book Religion and the American Constitutional Experiment is a good summary and helps provide an understanding of the somewhat surprising limited discussion of free exercise in Supreme Court opinions. This includes the argument "prohibition" should not be seen as a limited term, but one that guards against limiting free exercise as well. "Religion" is a tricky thing to define and the Supreme Court rarely tries to be specific. Witte offers "embraces a creed, a cult, a code of conduct, and a confessional community." I take it though that even a single individual can have a "religion" in some sense.
An early case involved polygamy and belief was separated from action: "while they cannot interfere with mere religious belief and opinions, they may with practices." But, the breadth of odium the opinion inflicts on polygamy suggests -- if it was around -- the ban would meet a "compelling interest" test, including to secure equality. Other cases involving mere advocacy of polygamy would be no longer good law. Some "animus" could be shown by the breadth of some of the legislation. The basic non-recognition of polygamy, however, might still hold though even in the 1940s some (dissent) realized some of the rhetoric against it was overblown.
The first cases handled by the Supreme Court involving free exercise in effect protected church autonomy such as in property disputes that turn on doctrinal disputes. Witte notes that part of "free exercise" was the right to join fellow believers in religious societies and have autonomy therein; this also would involve rights for religious motivated corporate bodies. Overall, this included religious worship, assembly, speech and so forth. Quakers would have the right to meet and so forth without special licensing being required. This would include religious education.
Various 20th Century rulings dealt with some of these latter matters, which overlap with other First Amendment provisions. Pierce v. Society of Sisters, e.g., allowed parents to send their children to parochial over public schools. Jehovah Witnesses had various cases involving public preaching, handling out leaflets (a limit here was child labor laws) and the like. Oregon v. Smith later treated allowing the Amish to only send their children to so many years of school as a "hybrid" right of free exercise and parental liberty. But, query if -- as I noted in the past -- if religious education is a core of free exercise so that it can be treated special even if the law in question is "general applicable"? A pass on all laws is untenable, but some sorts of coercion would be particularly problematic here.
The core of free exercise has been deemed freedom of belief, not singling out religious practice itself for discrimination (a sort of equal protection provision, more important before there was an Equal Protection Clause) and autonomy of religious institutions. "Belief" here would include speech and association, "speech" probably including certain symbolic actions or rituals. A few justices saw it as a matter of free exercise, but non-compulsion in respect to the flag salute was treated as a freedom of expression matter. I think the concurring justices had the best idea, especially since the Jehovah Witnesses were motivated by religious belief. Coercion to act here truly would in effect "prohibit free exercise."
Religious institutional autonomy along with various rights with a religious component provides limits to the "belief" v. "action" split that was reaffirmed in Oregon v. Smith. Equal protection also provides a barrier here to deprivation especially when fairly applied. Overall, however, "free exercise" would involve some sort of actions. Religious exemptions, especially in the area of military service, has continuously respected this fact.* The Constitution itself allows oaths and affirmations, respecting the religious beliefs of some in that area. Things were easier when there were less regulations and differences were basically among Christians.
Exemptions to major duties and laws that involve threats to the public order would have limits though. This continues with concern with harms to third parties in current disputes over state and federal RFRAs. The core of free exercise was and continues to be personal. As noted in Cantwell v. Connecticut, free exercise involves"freedom to believe and freedom to act. The first is absolute, but, in the nature of things, the second cannot be." Freedom to believe would involve various matters of expression and association. The "act" part is trickier. But such things as peyote use should be protected no less than handing out sacramental wine or intermingling of the sexes and races back in the day when that might seem a problem.
Peyote use is a somewhat easy call -- it is a sacramental act, a clear case of religious worship. Such acts, as seen by the child abuse scandal in the Catholic Church (and they weren't alone), are not by definition totally banned from state involvement. Marital rape can be addressed even given the privacy of marital bedrooms. Still, easy case, more to the core. Some do have a broader sense of religious duty as seen by the rules of Judaism and Islam where there is a bigger combination of the public and private. Religious duty is not limited to holy rituals and places.
It is therefore trickier to draw lines. We see this in the current controversy. A proper balancing can be made that respects all involved, free exercise in society not a matter of everything goes. To be cliched, this will result in some difficult questions, but the right answers (e.g., insurance that eases the ability to freely choose pursuant to one's personal beliefs) can further the free exercise of all, not just the favored class. An old story.
*Oregon v. Smith took notice, e.g., a category of cases where those who could not work for religious reasons still obtained unemployment benefits. This involved matters of the administrative state that respected individualized judgments, including exemptions. This was treated differently than general criminal laws where such exemptions were not as prevalent. Not that in practice there was quite such a clean line.
To me, the case would have been better left in that category, which is how the state courts handled it. Anyhow, here religious needs are treated along with other special situations. The greater involvement of government also leads to less possibility of clean separation of church and state. Free exercise in various cases, though simply treating religion the same as secular actors won't work either, would warrant equal treatment.