Newton does not refute St. Thomas on his own grounds; he just says in "Two Notable Corruptions of Scripture (part 1: ff. 1-41):"
[...] but to us Thomas Aquinas is no Apostle; we are seeking for the authority of greek manuscripts.(Cf. Fr. Ramírez, O.P.'s The Authority of St. Thomas Aquinas.) This "ressourcement" or "going back to the [supposedly] more authoritative sources" is what Modernist theologians say today. Modernism is detrimental to the advancement of science. In Standing on the Sholders of Giants, David Boyd Haycock writes (my emphasis and [comments]):
If Baconianism, Newtonianism and the Royal Society were three of the most significant influences upon the development of science in seventeenth- and early eighteenth-century England, then a fourth requiring full and equal consideration is religion. As we have seen, Baconian scientific methodology advocated a split from the earlier, uncritical Aristotelianism of the scholastics. However, in the Middle Ages Aristotelian philosophy and Christian theology had become thoroughly assimilated through the apologetics [He did pure philosophy and theology, too.] of the medieval scholar Thomas Aquinas, so that at least one cautious seventeenth-century religious commentator, writing as 'S. P.' (possibly Simon Patrick, later the bishop of Ely), feared that since 'philosophy and divinity [i.e., theology] are so interwoven by the schoolmen ... it cannot be safe to separate them; new philosophy will bring in new divinity.' [Yes, St. Thomas's doctrine on faith and reason will never be superseded.] It was this very fear which had led the Catholic Church to its persecution of both the former Dominican friar and philosopher Giordano Bruno [Suspected of the Arian heresy, he was a pantheist and materialist who said "Matter is not without its forms, but contains them all; and since it carries what is wrapped up in itself, it is in truth all nature and the mother of all the living." (C. Gutberlet).] (who was burnt at the stake [by civil authorities, not clerics] in 1600), and the Italian astronomer Galileo Galilei. Though English Protestants considered themselves well above such Papist extremes, Newton's critic Dr Edwards castigated his contemporaries for their practice of 'coining ... New Systems in Divinity.' He observed how 'this vain Apprehension [Yes, it certainly is vain. What is their justification of it?] possesses them, that, because in this Learned Age some parts of Humane Knowledge are censur'd [Such as?], and the very Principles of some Arts, especially those that relate to Natural Philosophy, have undergone a great Alteration [But not so great that, e.g., quidquid movetur ab alio movetur ("that which is moved is moved by another") is no longer true.]; therefore they may venture to advance some unheard-of doctrines in Divinity, to new model our Religion, to mend the Gospel, and to present us as it were with a New Christianity'. [So basically they changed "Divinity" in order to advance their supposedly greatly altered "Natural Philosophy," based on which they would try to justify the "New Christianity"?] Bacon had attempted to defend his new method from any such criticism by arguing that 'we do not presume by the contemplation of nature to attain to the mysteries of God.' [Cf. Romans 1:20: "For the invisible things of him, from the creation of the world, are clearly seen, being understood by the things that are made; his eternal power also, and divinity."] But it was impossible that a science based upon the empirical study of a world considered to be divine handiwork would not inevitably lead to questions relating to the very nature of the divine itself. [This is why by their very nature "philosophy and divinity are so interwoven," so, with Dr. Edwards, I reiterate: "Why the need for a 'new philosophy' and 'new divinity'?"]"Do not block the way of inquiry!", C. S. Peirce would say.