With respect to both vaccinations and withholding medical care, legislatures have enacted protections for religious objectors. But no court has ever protected such conduct under the Constitution.
Pandemic restrictions are like these examples. Covid-19 kills some and permanently injures others; the threat to human life is real and immediate. Those who flout the rules endanger everyone around them, and this is sufficient reason for regulating even a worship service.
Whether a particular regulation is justified depends on its facts. How widespread is the virus in these neighborhoods? Do the regulated zones closely correspond to places where the infection rate is significantly higher? What regulation is actually needed to save lives?
The governor should have to prove his factual claims in the Agudath Israel lawsuit. But assuming that he has the facts approximately right, then the new regulations are mostly justified. The devil is in the details.