I am sure they assumed that the “problems” that would cause them to leave would appear almost “instantly” not after roughly 3 generations. (Assuming a generation equals 25 years!)
What you say is true. Few of the original 13 would have ratified if they would have thought that it meant eventual submission to federal authority in all cases. The Civil War cemented the paradigm of U.S. supremacy over State sovereignty. This has led us to where we are today. The omnipotent federal state, consuming all political liberty and personal freedom.