I'm not a lawyer, but I have to say that I found the entire "limiting principle" discussion at the Supreme Court somewhat confusing. After all, if the government can charge you a 20 percent marginal tax rate what's to stop them from going to 39.4 percent or 99.7 percent? Nothing, it seems to me, and yet life goes on.
But Congress could, if it wanted to, completely vitiate economic freedom purely through the tax code. You would impose a statutory rate of 100 percent and then create deductions for the stuff Congress wants you to buy—houses, health insurance, broccoli, whatever. I don't think anyone would reasonably conclude from the fact that Congress could do that stuff that we do not in fact live in a free society in which individuals have a wide scope of choice over what to do with their selves, their time, and their money. But no level of Commerce Clause jurisprudence is going to guarantee that freedom as long as Congress has plenary authority to tax people. The scope of that taxing authority is a separate legal question from the scope of Commerce Clause authority, but if you're interested in the substantive question of human liberty you're still left with the fact that there are no guarantees outside of the ordinary congressional process. If a political consensus exists that Congress wants to financially penalize non-purchase of broccoli, Congress will find a way. In fact we do have a political consensus around financially penalizing the non-purchase of corn, and we implement it through general taxation followed by direct government payments to corn-growers. Encouraging people to eat more broccoli would at least make some kind of sense.
UPDATE: I see Akhil Amar who is a lawyer makes precisely this point about a 100 percent tax in a Wonkblog interview.