The words of the inquisitor were right at one point, though wrong on geocentricity. The words of the Bible should be believed over that of Greek and Roman philosophers, who truly knew nothing. Philosophy is like a dog chasing its tail. It never goes anywhere. Never reveals truth. Just lives in perpetual cynicism. The one who made Heaven and Earth knows everything, and reveals enough of the truth that we should trust him, and gave His Son to die that the sins of those who trust in Him will be forgiven, and will receive eternal life.

If you study Church History, you will learn that the Church made a lot of errors that obscured the truths of the Bible. 1) Restoring the Levitical Priesthood. 2) Saying Marriage is a lesser state, and denying it to Church officeholders. 3) Transubstantiation. 4) Geocentricity. 5) Restricting the Bible to Latin. 6) Works being meritorious for salvation. 7) Purgatory. 8) Aristotelian Philosophy. 9) Letting Tradition impair the clarity of the Bible. 10) The Papacy, because our one true High Priest is Jesus, who brooks no competitors. Competitors are Antichrist. 11) And there is much more... this manga is right to criticize the Church with respect to geocentricity. Nonetheless the Bible is true, and the Church was wrong to ignore it.