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The thing is, as of the time the law was passed, *everyone* across the political spectrum thought this thing was constitutional. The Heritage Foundation started it, the D's finished it, and the whole way down no one thought it ran afoul of the Constitution (save for people considered fringe at the time).
What this says is that Congress and the entire country were relying on the precedents SCOTUS set to pass the law--and they spent almost two years and untold legislative resources doing it. That's the whole point of stare decisis, allowing for predictability with respect to what the law allows. Stare decisis is what makes sure the courts don't act arbitrarily by constraining them to fit within precedent.
Acting in ignorance or with disregard for precedent (and precedent's practical attendants, like reasonable beliefs in the public about what the law is) undermines rule of law, makes it impossible to pass laws confident of their legality, etc. It is, in a word, arbitrary. It's the kind of thing they do in developing countries.
If SCOTUS ditches stare decisis here, sure their credibility will take a hit, but more importantly: we, as a polity and individuals, would have no reason to think we could pass any major regulatory legislation (unless, of course, we took the political commitments of the justices as our guide). SCOTUS would be potentially freezing the statutory law in place. What is Congress supposed to do with its time if everything it thought it knew about the law gets chucked out the window? How does it pass legislation? How does it change *existing* legislation? Are only Republican Congresses allowed to pass laws?
Stare decisis and all the reasons we follow precedent command that the mandate passes. I've already gotten overly maudlin, but if the mandate is overturned, we're ruled by men, not laws.