In a little-noticed portion of his 73-page dissent, Judge Wynn rejected free exercise, RFRA and Establishment Clause challenges to the statute, saying:
Appellants allege that the Act compels them to violate their “sincerely held religious beliefs against facilitating, subsidizing, easing, funding, or supporting abortions” and prohibits the University from “providing health care choices for employees that do not conflict with the mission of the University and the core Christian values under which it and its employees order their day to day lives.”... This argument is unavailing.... The Act is a neutral law of general applicability and so does not violate the Free Exercise Clause....
I also reject the claim that application of the individual mandate to appellants would run afoul of the Religious Freedom Restoration Act of 1993 (RFRA).... The [Affordable Care] Act contains provisions to ensure that federal funds are not used for abortions (except in cases of rape or incest, or when the life of the woman would be endangered).... and that each state’s health benefit exchange will include at least one plan that does not cover (non-excepted) abortions.... I cannot say that appellants’ complaint makes it plausible that the Act “substantially burdens [their] exercise of religion.” ...
Appellants also challenge the Act’s religious exemptions themselves, claiming that they violate the Establishment Clause and equal protection because “they grant preferred status only to certain religious adherents.”... The religious conscience exemption simply incorporates the exemption created by [26 USC] section 1402(g)(1), which has survived every Establishment Clause challenge to it over the last forty years.... The exemptions easily survive appellants’ equal protection challenge as well.