Debunkers didn't just appear during the advent of modern science. They've been around for a long time. And although some debunkers can be quite annoying when they are cynical skeptics with a zealous belief in materialism, debunking isn't always bad. Sometimes its good to have a debunking attitude, as long as you don't take it to a zealous extreme.
One well known Renaissance debunking is that of geocentrism. The heliocentric model is taken for granted today, but for a long time, many people adhered to a geocentric model of the universe. The idea that the Earth revolves around the Sun was actually proposed by Aristarchus of Samos in the third century BC, but Nicholas Copernicus further developed the heliocentric model in the 16th century. Johannes Kepler supported the heliocentric model and Galileo contributed to it with astronomical observations he made using his telescope. Isaac Newton also supported the heliocentric model. Eventually, it was accepted that the Earth was not the center of the universe, and not long after that, astronomers began to realize that the Sun wasn't the center of the universe either. I suppose if the universe is infinite though, then maybe it doesn't really have a center. With that in mind, I guess it's really a matter of opinion where the center of the universe is.
It took a long time to debunk geocentrism and debunking it cannot be attributed to any one person. But there is a debunking from the 16th century that didn't take quite as long. The Rood of Grace, also known as the 'Holy Cross of Grace', was a wooden image of Jesus on the cross that was supposed to be miraculously gifted with movement and speech and was housed in Boxley Abbey in England (a rood is a large crucifix on a beam or screen at the entrance to the chancel of a church). It was during the 16th century that the Protestant Reformation began and King Henry VIII of England broke ties with the Catholic Church in Rome. It was during this atmosphere of anti-Catholic sentiments that the supposed miracle of the Rood of Grace was debunked. Thomas Cromwell sent Geoffrey Chambers to close down the abbey and investigate the rood for him. Chambers reported back that he found “certain engines and old wire, with old rotten sticks in the back of the same that did cause the eyes to move and stare; and also the nether lip to move as though to speak.” The abbot and monks claimed to be ignorant of it, but Chambers exposed the hoax and the Rood of Grace was burned in London. I suppose it might be possible that the monks at Boxley were not intentionally deceiving pilgrims visiting their abbey, but I doubt it. I think it's most likely that the monks (or at least one or some of them) knew what they were doing and were intentionally deceiving pilgrims so they could influence them and get money from them.
Another example of a historical debunking comes from ancient times. The story of Bel and the Dragon, an apocryphal addition to the book of Daniel, describes a debunking. Daniel is employed as a chief advisor to the King of Persia. Daniel, who was an exiled Jew, refused to worship Bel. The King questioned him as to why he refused to worship Bel and pointed out to him that the idol of Bel would eat all the food and drink all the wine that was left out for him at night. Daniel claimed that the idol was not really eating the food and drinking the wine at night, but the priests of Bel continued to say that Bel was eating the food and drinking the wine. The King declared that Daniel would be put to death unless he could prove that the priests were lying. So to prove he was right, Daniel spread ashes out on the temple floor that night before the King sealed the doors to the temple. The next morning when the King opened the door and saw all the food had been eaten, Daniel pointed out footprints on the floor. The King saw the footprints of men, women, and children on the floor, and he demanded the priests show him where the footprints came from. The priests showed him a trapdoor hidden under a table. The priests had been coming in at night with their families to eat the food and drink the wine. It was not the idol of Bel eating the food afterall. Daniel's life was spared.
Even if this addition to the book of Daniel isn't true, I think it's at least clear that some ancient author understood the concept of debunking.
Archaeological evidence suggests that some clever pagan priests from ancient times were able to deceive worshipers by hiding behind an idol and speaking through a hole, giving the worshipers the impression that the idol was talking. Hero of Alexandria, an ancient Greek inventor, built a primitive steam engine that could pull the doors of an ancient temple open using pulleys. To worshipers, it may have appeared as though the god of temple was miraculously opening the doors.
So although debunkers and skeptics can sometimes be annoying, I think these examples show that debunking can be a good thing. The key to a good debunking is to keep an open mind and not take the debunking to a zealous, materialistic extreme.