'The Penaltax: A Problem Here?

As I was driving through western South Dakota yesterday evening, this blog post by Dave Birge set off such a mental fugue in my head that I forgot to look at my fuel gauge and almost ran out of gas.

Here is what I haven't quite figured out.  First, the facts:

The Affordable Care Act at one time, so they say, had language that described the penalty for refusing the buy health insurance when the government says you can afford it as a "tax."  That was taken out, many people think, because the bill could not have become law if this charge, cost, impost, whatever it is, is a tax. If it was, it wouldn't have gotten through Congress. It had to be a penalty, not a tax.

Then, in the Supreme Court, it became a tax again.  Why?  If it were a penalty, it would not have gotten through the Supreme Court.  This is certain.  Unless Chief Justice's discussion of the Commerce Clause argument was a blatant lie, he was bound to side with the three other conservatives and Anthony "Swing Vote" Kennedy and strike down the individual mandate.

So in order to get through Congress, it was a penalty, and in order to get through the SC, it was a tax.  All the Republicans seem to have to say about this (not including Romney in this case) is something like "Aha!  So you did raise taxes!  So there!! Nyah nyah!"  Am I the only one who sees a deeper problem here?  Does anybody see any "checks and balances" issues here?  Something about the rule of law?  Anybody?  Anybody?  Hello?

I haven't quite put my finger on it yet, but I think there's a problem here:  A law means whatever it has to mean in order to get passed and stand.