Why? If you've got a wild enough imagination to take things this far, why does it fail you now?
Gerry mentions the dissolution of the states and the possibility of civil war and no one notices and Madison mentions disunion, and everyone is shocked?
The fact that the convention rejected Madison's wish to have the highest militia officers appointed by the federal government doesn't mean that they believed unilateral secession was a good thing.
That would be like saying that all the anti-Federalists were opposed to union, justice, domestic tranquillity, common defence, general welfare, and the blessings of liberty for themselves and their posterity because they voted against the Constitution.
You can reject one suggested means to an end without rejecting the end itself.
It hasn't failed. At least I have one.
Gerry mentions the dissolution of the states and the possibility of civil war ...
Gerry is saying that IF the convention were contemplating dissolution of the state governments, instituting a king and House of Lords, THEN he could understand the attempt to delegate to the federal government the power over the militia. The British status quo. But he wondered why Madison was attempting to grant to the federal government powers that threatened the existence/sovereignty of the states. If that was the intention of the convention, then Gerry warns that those proposing such would likely be planting the seeds of war - the people that just fought a war for independence were not likely to bind themselves to another despot or tyrant.
and no one notices ...
Madison noticed. Other delegates had refused to attend the convention, Rhode Island and Providence Plantations refused to send delegates, and others left in disgust. Some framers were just wary of placing too much power in the hands of a single person or government. To allay Gerry's fears Madison opines that dissolution/secession was the great evil, and advocates again for federalization over the militias, along with any other powers to prevent it, and maintain the union by force. Madison couldn't even convince his own state delegation to vote for the measure.
You can reject one suggested means to an end without rejecting the end itself.
Which explains 9 states rejecting Madison's insane motion. They still wanted a new government, just not one that bound them by chains or military force, one that had no power to prevent their secession.