Interestingly, I think Roberts would agree, which is why he based his decision on what he thought was the more narrow reading of the taxing power, as opposed to a further expansion of the interstate commerce clause. It seems to me that the dissent you cite is really better argued against an expansive interpretation of the interstate commerce clause, and the Medicaid expansion. Kennedy’s argument against the tax portion of Robert’s decision is really pretty simple: it’s not a tax. It’s a penalty. I think that has less to do with arguments regarding structural safeguards on liberty, and more to do with how to define a tax. Of course, a broad reading of what constitutes a tax could be viewed as an erosion of liberty, but the cure to me seems not to lie in structural safeguards, but in a more narrow reading of what we mean by a tax.

I think the conclusion of the dissent by Kennedy, Scalia, Thomas and Alito says it best:

See page 191 of the decision

The Constitution, though it dates from the founding ofthe Republic, has powerful meaning and vital relevanceto our own times. The constitutional protections that this case involves are protections of structure. Structural protections-notably, the restraints imposed by federalismand separation of powers-are less romantic and have less obvious a connection to personal freedom than the provisions of the Bill of Rights or the Civil War Amendments. Hence they tend to be undervalued or even forgotten by our citizens. It should be the responsibility of the Court toteach otherwise, to remind our people that the Framers considered structural protections of freedom the most im- portant ones, for which reason they alone were embod-ied in the original Constitution and not left to lateramendment. The fragmentation of power produced by thestructure of our Government is central to liberty, and when we destroy it, we place liberty at peril. Today’sdecision should have vindicated, should have taught, thistruth; instead, our judgment today has disregarded it.

His tax-for-constitutional-purposes-penalty-for-AIA-purposes reasoning was also a huge incoherent mess in my opinion; it appears he wanted to uphold Obamacare even if he had to pull out a flimsy and unprecedented rationale, which nobody took seriously from the outset in the district courts, to justify it.

I obviously don’t have an answer, but I wonder 50 years from now whether Roberts’s rather surprising opinion will be remembered as having ‘saved’ the Court’s institutional reputation or opened a Pandora’s Tax Box. Roberts might have stealthily shut the door on further expansion of the Commerce Clause power (it was quite entertaining to see Ginsburg call him out on it in her opinion), but he waded right into the muddled waters of the tax power.

The problem is that there really is no judicially manageable standard to determine when a tax becomes a penalty (5%, 10%, 50%, 99.99%?, e.g. cigarette taxes). All taxes inherently have some regulatory effect. So although Roberts argues that Congress has a diminished capacity to compel certain activity from citizens, that contention wholly depends on future courts striking down punitive taxes according to an arbitrary judicial standard. See the different results in Bailey v. Drexel Furniture Co. and United States v. Kahriger.