Commerce clause says that the federal government shall be able to regulate interstate commerce. Pot is something traded in intestate commerce. Its not as ridiculous as you make it seem. The framers might have used narrower language if they could foresee that one day, everything would be a part of interstate commerce. That certainly wasn't true during the time of the framing, when goods were produced locally or even primarily by the individuals using them on family farms. But they used broad language with the intent of giving the federal government the power to regulate large scale commerce as it existed then.
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.