In what sense, if any, is the idea of a Revolution of 1800 justified?

Is justified by a change of paradigms. The idea of a nonpartisan polity fell and gave room for the party system similar to what we have today.

People voted for a president and the second in votes would become his vice-president; that changed in 1801, since that was a draw between Burr and Jefferson, evidencing a flaw in the elections system of the Constitution, so the people began to indicate who they wanted for each office.

If before the federalists had an hegemony, now the democrats, through Thomas Jefferson pursued great changes, it seemed like the previews federalists governments, Washington and Adams, failed to install policies that would benefit the majority of people. They seemed, at the time, like an elected "monarchy", with much centralized power distributed between the senate and the executive. The idea was that only a strong central government would garantee a prosperous, secure nation.

In the democratic proposal, the government would be for the people to rule / decide what was best for them, "The will of the majority, the natural law of every society, is the only sure guardian of the rights of men," Jefferson wrote in 1790. His idea / speech of a strong government was it to be "wise and frugal" to preserve order among the inhabitants, but would "leave them otherwise free to regulate their own pursuits of industry, and improvement."