The Supreme Court didn't say that corporations are people. It said that people don't lose their first amendment rights because they assemble themselves into a corporation. Falls naturally out of the first amendments rights to free speech and assembly.
You can't ignore the civil war. The 13, 14, and 15 amendments were a renegotiation of the Constitution at the point of a sword. The idea of a federation of independent states is called into doubt by the supremacy clause and commerce clause, which was in the original, and the 14 amendment, which allows Congress to legislate directly against the states to enforce the amendment. Moreover, looking at original intent, the federalist faction of framers wanted a strong central government. They didn't give states autonomy because they wanted to, they did it because they had to, and they set the stage for states becoming secondary powers.