Good question -- some Korean historians ask that question to themselves, I guess. I don't have an answer, but major peasant rebellions (yellow turban or taiping style) would happen in the 19th century

In the 17th century... right after the war... umm perhaps peasants were just way too starved and devastated to do anything. After the war with Japan, there was a major epidemic that further plagued the nation. Seeing dead people or even families on the street was common. Afaik, both French Revolution or Yellow Turban happened when the economy and communities were relatively healthier

Plus, there was little merchant class because of the suppression of trades. And aristocrats were very heavily controlled by the fundamentalist Confucian ideology to be loyal to the king, and they had substantial ideological control over peasants through provincial, village-level institutions.

After the war with Japan, in late Joseon, oppression on women would also exacerbate. So perhaps the village societies chose to enhance social control rather than revolt