While the word secession is not mentioned specifically in this instance, Mr. Madison's notes from June 18, 1787 contain a synopsis of a lengthy speech from Mr. Hamilton regarding the states' sovereignty and about his concerns that the states will be powerful enough to dissolve the union, but not the other way around, etc. So the idea of states backing out or dissolving the union was certainly a concern of his, and he made his concerns known. I believe he also touched on similar issues in one of the Federalist papers.
On a side note, at the end of his speech, Mr. Hamilton provides a list of recommendations for items to be included in the Constitution; some of which made it in in some form and some of which didn't. The most interesting to me (one which did not make it in) is a suggestion that the "General Government" appoint the Governor of each State, as part of an effort to assure that no laws would be passed in the states which were contrary to the constitution. THAT would be an interesting one to have practiced today.
I'm still looking for others.
That was always one of Hamilton's greatest worries. He knew the danger to the whole Empire of Liberty he strove for was an ability to walk away. A statesman of his foresight also knew that not one of the states could be able to seperate without absorption into one of the empires contesting for the continent.
This was one of the most weighty of the reasons Hamilton and Madison had worked incessently since 1782 for the Convention. Strengthening the Union "a more perfect Union" was the ONLY concern of the Convention. This impulse is utterly incompatible with the idea that unilateral seperation was even conceivable to them except as the most deadly of threats to the Empire of Liberty. Using extra legal means and open warfare would have been even more inconceivable given the excuse for revolution, oppression without representation, simply was not present in any form.
Hamilton gave the longest speech of the Convention and tried to push it as far to the right as he could believing that the great danger was weakness "imbecility" in the national government. But interestingly enough Madison at that time was more Hamiltonian than Hamilton and made equally radical suggestions for curbing the states power of the states and centralizing power. Hamilton's remark about the problem of using federal military intervention during the debate wherein Madison advocated just that. Only after Jefferson's return did Madison swing left and into, imo, error. Hamilton played "Bad Cop" very well at the Convention and drove a compromise which just barely strenghtened the government sufficiently to survive.