Requiring a supermajority is just privileging the side that prefers the status quo.
Rather, requiring a supermajority is to privilege the status quo, period. There are benefits to stability, no matter how it's constituted. These benefits are codified through mechanisms like supermajority votes.
A more rational referendum would have been a far more serious endeavor, perhaps one in which the population voted multiple times.
Big changes should, in general, not be easy to make.
I don't think citing that line of thinking (by Hamilton and Adams and the others) says a whole lot. It is, perhaps, ironic, that this line of thought was driven by the belief the British system of government was the best in the world. (Incidentally, during that time period, the 'three branches of government' were considered to be the House, Senate, and Presidency, not the legislative, judicial, and executive.)