There are many issues that lead to the Ming Dynasty's fall, but the Japanese invasion of Korea wasn't one of them. Better culprits would be corruption, famine, a Ming government that couldn't come to a consensus, and the Qing dynasty. Corruption is always present, and so that can't be considered the cause by itself. Famine occasionally occurs, and the Chongzhen slough that hit the Ming wasn't the first slough either. Because corruption and famine occur routinely in Ming history, they form a base for Ming failure but aren't sufficient reasons for the Ming fall.
If I had to choose a starting point, I might choose the Wanli Emperor's desire to choose his third son as Crown Prince. This was against the norms of the dynasty and opposition by the ministers paralyzed much of the government. There was also the Taichang Emperor's early death, which allowed for the weak Tianqi Emperor to be controlled by the eunuch Wei Zhongxian. That in turn allowed for incredible factionalism. After that, with things like the Donglin faction meant the government just couldn't come to an agreement.
The revolts before 1642 were rather limited and had frequently been crushed, only to roar back as strong as before. They were mostly limited to the Shaanxi/Shanxi area and consisted of roving bandits. They got worse after 1642, but these were only light rivals to the Ming legitimacy. They rarely managed to hold the land or the cities, and could have been crushed if the Ming didn't need to worry about the Qing. The issues were that the Ming never took these rebels strongly because of the worry about the Qing, and commanders in the field were never honest about the issue either. So Ming armies would fight the rebels, and would report a victory whether they won or lost, so the government would consider the issue settled, and thus never realized the issue they were in.
When the Ming went up against the Qing, it found itself outmatched at the state level. The comparison doesn't need to be extended too far: the Qing knew how to run a government and the late Ming did not.
Various other issues that contributed: the Ming had an imperial nobility that turned out to be an incredible drain on resources. There was also the fact that the Chongzhen Emperor was not an extremely decisive ruler. This was especially problematic since the Ming government centralized power in the ruler and in the 1640s there were no powerful ministers capable of bending the government to their will. So by the very late Ming, the government lacked strong decisive leadership. Also, even after the Ming fell, a southern remnant in the form of the Southern Ming could have held a while longer, but this collapsed due to Qing superiority during the Qing conquest, as well as because of infighting between different Ming claimants.
There were many reasons why the Ming fell. Taking away the Japanese invasions of Korea might lead to butterflies. For example, maybe if the Japanese don't invade, the butterflies mean the Wanli Emperor dies soon after appointing his son, the Taichang Emperor, who rules better than his father and avoids the Wei Zhongxian dictatorship. But the Japanese invasions are not the cause of the Ming Dynasty's fall at all. There were many more direct reasons.