He outright says the opinion assumes that the issue in the case, providing abortificants, does serve a compelling government interest. That appears at point (c) in the Syllabus (but NEVER trust the syllabus). Attributed to Alito and the majority:
Under RFRA, a Government action that imposes a substantial burden on religious exercise must serve a compelling government interest, and we assume that the HHS regulations satisfy this requirement.I don't take that as agreement with the premise, beyond "assume for the sake of argument." The majority's focus is on the "least restrictive means" requirement, and it is failure on that prong that results in the abortificant mandate being against RFRA.
HHS responds that many legal requirements haveexceptions and the existence of exceptions does not initself indicate that the principal interest served by a law isnot compelling. Even a compelling interest may be outweighed in some circumstances by another even weightierconsideration. In these cases, however, the interest served by one of the biggest exceptions, the exception for grandfathered plans, is simply the interest of employers in avoiding the inconvenience of amending an existing plan. Grandfathered plans are required “to comply with a subset of the Affordable Care Act’s health reform provisions” thatprovide what HHS has described as “particularly significant protections.” 75 Fed. Reg. 34540 (2010). But the contraceptive mandate is expressly excluded from this subset. Ibid.
However, just to get on with the discussion, he goes to least restrictive means, because he's certain the government has erred in that category, so the argument over compelling interest is of no real import.
We might be saying the same thing.