The reason they didn't go after van Leeuwonhoek was because the Roman Catholic Church wasn't hugely concerned with people's scientific views. There were plenty of early astronomers who were able to create and discuss new ideas without being suppressed by the Church. Copernicus was a cleric, and was supported in his studies by several senior figures within the Church. Tycho Brahe became court astronomer to the Catholic Holy Roman Emperor. Similarly, his successor, Kepler, was able to be court astronomer to three separate Emperors, despite his Protestantism. The two big figures that are pointed to as evidence for Church suppression of astronomy are Giordano Bruno and Galileo. Bruno is a poor fit - his cosmology was based completely on guesswork, and much of it looks ridiculous to modern eyes. He was burned not for his scientific views, but instead for his rejection of several major points of Catholic doctrine, mainly relating to theological matters such as the divinity of Christ. Similarly, Galileo was censured less for his scientific views and more for religious and political matters. While part of the problem was his publishing his claims for heliocentrism, which he had no evidence to support, his bigger crimes were reinterpreting the Bible, and ridiculing the Papacy.