The SCOTUS ruling corrects an infringement on the free exercise clause and does nothing to harm the establishment clause.
CFI and RDFRS issued a joint statement that is very poorly reasoned.
CFI says:
“CFI Legal Director Nicholas Little said, plainly, “The Supreme Court has detonated a massive breach in the wall of separation between church and state.” He went on to say, “We are deeply concerned about what happens next, as other sectarian organizations find new and novel ways to siphon taxpayer dollars into their churches, temples, and mosques." "
Our First Amendment says:
“Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof”
Our Fourteenth Amendment says:
“No state shall make or enforce any law which shall abridge the privileges or immunities of citizens of the United States; nor shall any state deprive any person of life, liberty, or property, without due process of law; nor deny to any person within its jurisdiction the equal protection of the laws”
The majority held in Trinity Lutheran v. Comer:
The Department’s policy violated the rights of Trinity Lutheran under the Free Exercise Clause of the First Amendment by denying the Church an otherwise available public benefit on account of its religious status. Pp. 6–15.
(a) This Court has repeatedly confirmed that denying a generally available benefit solely on account of religious identity imposes a penalty on the free exercise of religion
Thus, Trinity Lutheran v. Comer was rightly decided. CFI and RDFRS are mistaken. SCOTUS has not attacked the establishment clause, rather, SCOTUS has overturned a violation of the free exercise clause.
The establishment clause is still fully in force.