Clarence Thomas even worse than I thought, and that's saying something.

[Ms. Toad]

11. The article not only mischaracterizes what he said,

it ignores the basis on which he dissented.

First - his dissent says nothing about how he would have decided the case - merely that he believed the court should hear it.

As to the basis of dissent, it is a refinement of the Smith argument (which I discussed here).

There were two categories of individuals who were not vaccinated: Those with medical exemptions and those with religious exemptions.
Those with medical exemptions were permitted to continue working - as long as they took certain precautions to protect others. Those who asserted religious exemptions were not permitted to continue to work - even if they took identical protectinos.

That distinction is what Thomas wanted to explore.

Generally - Smith - says that the state doesn't have to create religious exemptions to a generally applicable law which was not drafted to target the free exercise of religion. (In Smith - at issue was whether the state had to accommodate Smith's use of peyote in religious ceremonies in the face of a generally applicable law which prohibited the use of peyote.)

Last year the court decided that a law was not generally applicable:

if it prohibits religious conduct while permitting secular conduct that undermines the government’s asserted interests in a similar way.

https://www.supremecourt.gov/opinions/21pdf/21-1143_3f14.pdf

I haven't read that case (Fulton v. Philadelphia), and don't recall it off the top of my head - so I don't know how similar it was. But the argument here is that because NY created a secular exemption to vaccines (for medical reasons) but refused to accommodate religious beliefs in the same way, the law is not generally applicable. If it isn't generally applicable, then applying the law differently to those asserting religious beliefs than it does to those asserting secular beliefs, violates the free exercise of religion.

Whether the Catholic Church believes there are no legitimate religious objections to using the vaccines is completely irrelevant to the argument the petitioners made. The question is whether an exemption available for secular reasons can be barred when the asserted basis of the exemption is religious.

Note: This explanation is a legal one. It is not a statement of my belief, or even of how I think the case would be decided. It's just an explanation of the legal basis for the dissent - and how the question raised fits within prior case law.