As most people do, you are misreading the Supremacy Clause. Here it is, with they key phrase that reverses the meaning from what you think it is in italics:
This Constitution, and the Laws of the United States which shall be made in Pursuance thereof ['thereof' refers to the Constitution]; and all Treaties made, or which shall be made, under the Authority of the United States, shall be the supreme Law of the Land; and the Judges in every State shall be bound thereby, any Thing in the Constitution or Laws of any State to the Contrary notwithstanding.
Unconstitutional laws are emphatically not "made in Pursuance" of the Constitution. And that's the whole point at issue in this case.
It is logically and legally invalid to simply assume the truth of a disputed point (whether or not the law is Constitutional) to decide whether the State has standing. The Supremacy Clause can only be used to decide a legal issue once the determination has been made that the law in question is Constitutional (unless the Constitutionality of the law is not in dispute—which it is, in this case.)
I agree with you that the term “pursuance” is the key. I totally understand that. I feel ObamaCare is unconstitutional and a perversion of the Commerce Clause.
The reality of the matter though is that the constitutionality of federal laws are decided in federal courts and not in state courts or by state level officials. I agree that the state of Virginia has an extremely valid argument that the mandate is unconstitutional but until the Supreme Court strikes down the mandate or Congress were to hypothetically repeal the mandate then the Supremacy Clause is for all legal purposes binding on the Virginia law.