I believe he actually believed the Union came before the Constitution, which supports the actions to usurp it.
Actually, IIRC, the 'union predating the states' was later Hitler's interpretation of Abe's view.
If your political solution to the North-South controversies of the 1850's were jammed up by constitutional prohibitions -- such as against waging war on a State -- then you'd have to, in the immortal words of William Jefferson Clinton, find a way around the Constitution, wouldn't you?
As shown by other posters on another thread, Lincoln had support for his view from prominent Hamiltonians like John Jay and John Marshall. These Hamiltonian Supreme Court justices never accepted the People's rejection of their idea of national amalgamation and dissolution of the residual, and ultimate, sovereignty of the States. They handed down numerous weasel-worded Supreme Court decisions dealing with sovereignty and Supremacy Clause issues not from a constitutional basis, but based on (and enunciating as dicta) Hamiltonian theories of where sovereignty lay, and the nature of the People.
Lincoln was also supported by contemporary (to him) law writers like Thomas (?) Sergeant (cited in prominent law dictionaries of the day), who enunciated the Hamiltonian snow job as if it were the law of the land, when it wasn't and never had been.