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.
If Alito had really gone out of his way to address this, the opinion would have found the mandate fails on either prong. Or, at least add a "for the sake of argument" before saying the majority assumes the mandate serves a compelling government interest.
Even if you and I have a difference of opinion on whether Alito went out of his way to indicate the government really didn't have a compelling interest (and I don't think we have much of a difference), it certainly has no play in the outcome here, but I wonder if the "assumption" might come back in some other case (not necessarily before SCOTUS) and be used to justify a different HHS regulation.