Yesterday in class, Hannah raised the question posed by then-Justice Rehnquist in his dissent in Philadelphia v. New Jersey: how was New Jersey's out-of-state solid waste ban any different from state quarantines, which the Court had previously upheld. I tried to answer her question, but I could tell my effort was not terribly successful. Let me explain further now.
In the quarantine situation, the state is attempting to completely bar or eradicate some noxious agent from within its borders: hoof and mouth disease, the Mediterranean fruit fly, or whatever. To eradicate this menace, the state takes a few complementary steps. First, it takes action to destroy its existence within the state's borders. Second, it bars anything from coming into the state that might contain the agent. (This second step, of course, is the quarantine that has been upheld on dormant Commerce Clause challenge.) The quarantine is constitutional because, when seen in context, it is part of a nondiscriminatory effort to completely eradicate or eliminate the destructive agent from within the state's borders. (Alternatively, you could say the state has no non-discriminatory alternatives to accomplish this aspect of its objective.)
Contrast that with how New Jersey approached the problem of solid waste. It did not think that the existence of solid waste per se within its borders was a public health problem. Nor did it think that the disposal of solid waste within its borders was a public health problem. Instead, it wanted to reduce the amount of solid waste disposal within its borders. This is a perfectly legitimate objective, but it cannot be pursued in a discriminatory fashion. New Jersey cannot pursue its goal of having less solid waste by placing the burden of that reduction entirely on out-of-state waste producers.
A more analogous case would be if California, instead of wanting to completely eradicate the Mediterranean fruit fly, only wanted to reduce the size of its population. And pursuant to that goal, the state sought to accomplish that objective through a law that discriminated based on geographic origin -- for instance, by prohibiting the importation of fresh fruit. Even if such a measure would reduce the fruit fly population, California could not accomplish that goal by foisting the burden on fruit farmers entirely on out-of-state producers.
In short, in the quarantine cases the state's objective, though similar, was qualitatively different: complete eradication. Seen in that light, the bar at the border was effectively nondiscriminatory. Persons trying to bring diseased cattle into the state were really treated no differently than in-state residents who owned cattle that the state learned were diseased.