The decision before the court was described this way by SCOTUS Blog:

(1) Whether the provisions of Executive Order 202.68 by Gov. Andrew Cuomo (D-N.Y.) that limit in-person “house of worship” attendance to 10 or 25 people, but allow numerous secular businesses to operate without any capacity restrictions, violate the free exercise clause; and (2) whether the courts below erred in concluding that Jacobson v. Massachusetts and South Bay Pentecostal Church v. Newsom require the application of a deferential, rational-basis review in all cases challenging government action taken in response to a public health emergency, even when fundamental rights such as free exercise are at stake. //

Cuomo’s argument for lockdowns before SCOTUS provided no evidence that religious gatherings were actually spreading the disease.