>You imply the known japanese are native to Japan
Because they are. As native as "came to the island some 15,000 years ago, intermixed with another group about 3,000 years ago" can get, anyways. I hope you're not a serious believer in the Gook royal family theory.
>and the non-buddhists respected farmers, they did not.
This is your brain on anime.
Many of the necessities we take for granted today like food and salt were hard to come by before the introduction of chemical fertilizers in the 1800s, and many of the luxuries we take for granted like iron were as expensive for the Japanese as something like Indium is today. I'm not going to get into early Japanese history because it should be fairly obvious how a group that are described by the Chinese as "a bunch of filthy farmer HikkiNEET runts that like to get drunk and have weird but strict social etiquette, and who stuck a woman in the emperor's seat so that everyone would stop fighting" would not be in-line with this idea. Equally I will gloss over everything from the Heian period until Nobunaga's time because Samurai frequently worked alongside farmers since Neo-Confucianism had not taken hold yet
and being able to feed yourself was as important as your honor was. The only point in more "modern" history (last roughly 500 years) where farmers were treated exceptionally poorly was during the series of civil wars in the 1500s which almost starved the nation to death.
Usually people associate Hideyoshi's reign with images of the earlier 1500s because it makes for cool anime and storytelling, however in reality Hideyoshi was a statesman and a military man focused on establishing a strict hierarchal society. Hideyoshi is also the one who took everyone's weapons and paved the way for the Tokugawa Shogunate. Up until then peasants were heavily armed, so it's easy to vilify the Samurai under his rule since they suddenly no longer had to worry about being poked to death with sharp sticks. Most people don't understand the difference, but a Samurai was a government worker in a sense while RONIN (浪人, literally "drifter") were the ones going around murdering peasants. These ronin stalked the countryside roughly from the time the Daimyo system was established until about the end of the Tokugawa Shogunate, but they were generally seen as little more than bandits and vagrants with swords and sharp sticks until Ieyasu. When Ieyasu took power, he eliminated several Samurai houses while establishing Neo-Confucianism, which led to a mass increase in the number of ronin. They became endemic upon the early Tokugawa Shogunate and were rightfully pissed at having their land or houses taken away, and in response the ronin took out their anger on peasants quite often since they felt they still had their honor even though it was stripped from them. Ironic, because the samurai acted the same way during the Meiji restoration.
In addition, because of how Ieyasu balanced power under his rule, the Daimyo were significantly weakened and had to rely on proper book keeping and human resource managing of their territories in order to not lose their houses. This meant that farmers, who now had family names proving they weren't spies and lords who were investing in them, along with a lack of wars to fight, had an unprecedented level of power under the late-term Shogunate (after the ronin died of old age or got murderhobo'd by angry villagers), and were allowed to travel outside their territory for business/pilgrimages without fear of fucking dying.
At the end of the day farmers were at the bottom of a strict hierarchy through Japanese history, but so long as they respected that hierarchy they were treated fairly and could be expected to live long lives unless drafted into a war, but war was not particularly harmful to just farmers. Nobody got off the hook. They could not leave their territories because all
life was disposable outside of your hold during various time periods (especially the warring states period and first 50 years or so of the Tokugawa Shogunate). However the Japanese political class and samurai were not the ones killing farmers indiscriminately like you were implying. When a famine struck, it was tough times for everybody and tough times bring tougher times for those at the bottom of a social hierarchy. Famines were common until the Meiji restoration where Japan just stole food from other countries (until they could get ahold of chemical fertilizers anyways). I got a little off-track there, but my point was that farmers were victims of circumstance in times when everyone was suffering, and rarely victims of wanton violence or discrimination, since they were literally the bread basket of Japan that even saw their lords working beside them prior to Neo-Confucian class systems.