No it wasn't. Thomas Jefferson said he hoped the United States wouldn't be without a revolution like Shay's Rebellion every 20 years, but in the context of the letter in which he made that quote, he certainly didn't consider such an event to be legitimate. He was speaking to the spirit of revolution in the American people, not the intended design of the government.

If the American system were actually intended to operate as you describe, that intent would have been put into the Constitution.