The issue here isn't any "one size fits all" policy. It's such a policy when there are fundamental rights being restricted - which really isn't new. What's new is their application of an existing balancing test.
Governments can impinge upon constitutional rights in certain circumstances where the governmental interest is substantial enough (the classic example is "can't yell 'fire!' in a crowded theater" ). When courts evaluate individual rights against governmental interests (effectively group rights) they apply a balancing test weighing those competing interests. The more fundamental a given right is, the stricter the "scrutiny" that the court applies in evaluating a government action that restricts that right.
In the case of something as fundamental as the free exercise of religion, the courts apply a "strict scrutiny" standard. Which means that the action must meet a "compelling governmental interest"
Up until that point, it's likely that all nine justices agree. They likely also all agree that NY's interest here is compelling (public health). The disagreement (apart from whether the ruling is needed at this time at all) is in the third leg of the strict scrutiny test: the policy must be the least restrictive way of achieving the goal... with a little disagreement over the second leg (that it must be narrowly tailored to achieve that interest.).
For instance - NY has some really large churches. St. Patrick's can reportedly hold 3,000 people in a single service. Limiting them to 10 or 25 people at a time is arguably not the "least restrictive" when they could put several times that number in a service without risking anyone's health. If Cuomo said that churches in red zones were limited to 10% of capacity... then it would have been harder to make this ruling.
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