The question was not whether the state or federal governments can tax behavior but whether the individual mandate was a tax or penalty. No one argued that the government lacks the power to tax. Likewise the Supreme Court, while ruling that a tax can reasonably be construed to have the effect of a penalty, never have they ruled that a penalty can reasonably be construed as a tax. With respect to justifying a wrong with another wrong; the question should always be laid on its merits and if you are trying to point to inconsistencies in other similar but different cases you are not judging the case at hand on it's merits but justifying it via pointing to other "wrongs."
Again, I don't think g5000 is 'justifying' anything. I'm certainly not. The mandate is flatout wrong in my view, regardless of what you call it. But it is fundamentally no different than other tax incentives that pollute our tax code at all levels. I just think you're barking up the wrong tree in opposing it on technical nomenclature issues. The difference between a tax incentive and a tax penalty is entirely superficial. And in that narrow sense, Roberts was right to rule as he did.
Where the Constitutionality of PPACA, and the mandate, is questionable (apart from my general conviction that discriminatory taxation should be banned outright) is the fact that Congress deliberately used ambiguities in the language to deceive the public. The President and Congress repeatedly claimed the mandate was not a tax, presumably to maintain the ruse that they weren't 'raising taxes'. They knew there was really no difference between tax incentives and penalties implemented via taxation, and hoped the court would agree. But they avoided calling it what it was to limit public opposition. To me that's a kind of fraud, and I'd hope such a thing is unacceptable - to voters if not the Court.