Not really, see Smith v. Oregon Employment. en.m.wikipedia.org
The govt may trespass on religious freedoms where the offending the law is one of general applicability. Payote smoking generally applies to all persons and doesn't single out a specific religion. Govt may make this law.
Additionally, because of the supremacy clause, if the pastor is violating federal law (of general applicability), the feds may prosecute without violation of religious rights. The govt may not compelled the state to enforce the federal law though.