A second case, Eternal Word Television Network, Inc. vs HHS, dealing with the HHS mandate shows the impact of yesterday's SCOTUS decision.

An article, "EWTN gets last-minute stay on HHS mandate after Hobby Lobby decision," notes that because of the SCOTUS decision yesterday, the 11th U.S. Court of Appeals granted a injunction, pending appeal, against HHS enforcing crippling fines against EWTN, starting today, for their refusal to violate deeply help religious convictions and provide contraceptives and abortifacients. EWTN does not qualify as a religious employer.

While the COA three-judge panel did not issue an opinion on the ultimate merits of the case to be appealed, Judge Pryor, in his concurrence, most certainly did (Pryor's whole concurrance is worth reading):

The Network has asserted, without dispute, that it “is prohibited by its religion from signing, submitting, or facilitating the transfer of the government-required certification” necessary to opt out of the mandate. The Network further asserts that, by requiring it to deliver Form 700 to the third-party administrator of its health insurance plan, the United States has forced the Network “to forego religious precepts” and instead, contrary to Catholic teachings, materially cooperate in evil. Midrash Sephardi, Inc. v. Town of Surfside, 366 F.3d 1214, 1227 (11th Cir. 2004). If it fails to deliver that form, the Network faces $12,775,000 in penalties a year. 26 U.S.C. § 4980D(b)( 1). If that is not a substantial burden on the free exercise of religion, then it is hard to imagine what would be. …

It is neither our duty nor the duty of the United States to tell the Network that its undisputed belief is flawed. See Burwell v. Hobby Lobby Stores, Inc., No. 13-354, slip op. at 36-37 (U.S. June 30, 2014). The Supreme Court has instructed that “it is not for us to say that the line [drawn by the religious believer] was an unreasonable one. Courts should not undertake to dissect religious beliefs. . . .” Thomas v. Rev. Bd. of the Ind. Emp ‘t Sec. Div., 450 U.S. 707, 714, 101 S. Ct. 1425, 1430 (1981). The United States flouts that instruction by treating an undisputed religious belief as a disputed question of law. But “it is not for us to say that [the Network's] religious beliefs are mistaken or insubstantial.” Hobby Lobby, No. 13- 354, slip op. at 37. We must instead “determine whether the line drawn [by the Network] reflects an honest conviction, and there is no dispute that it does.” Id. at 37-38 (internal quotation marks and citation omitted).
[Emphasis added]