Continued Struggles.You see the problem here? Its not simply a matter of the caricature of Christians persecuting Jews. There were complicated dynamics at play, with Kings often at odds with the Pope in these matters, and Pope often sticking up for the rights of those who were being persecuted by mobs or the Crown or whoever.Under Clement's successor, Paul III., a friend to the Jews, the struggle concerning the Inquisition in Portugal was continued. King John, in whose interest the Spanish ambassador at Rome, Count de Cifuentas, and Cardinal Santiquatro were active, left no means untried to induce the pope to repeal the bull of his predecessor. ... Paul decided in Nov. (3 or 26), 1534, that for the present the "Bulle de Perdon" should not be published. He then submitted the matter for further careful investigation to a commission consisting of theologians and jurists, among whom were Cardinals Hieronymo Ghenucci, author of a work in defense of the Neo-Christians, and Jacobo Simonetta, one of the most learned men in the Curia. The majority of this commission expressed itself in favor of the Neo-Christians. At the same time the papal nuncio in Lisbon informed the Curia that the "Bulle de Perdon" had been published throughout the land, but that the king not only refused to liberate those imprisoned for their religious belief, but had made new arrests and had renewed(June 14, 1535) for three years the law of July 14, 1532, prohibiting emigration.
With John, as with his father Manuel, the chief concern was the property of the Maranos; and for this reason neither father nor son wished them to leave the country. The former desired to baptize them; the latter, to burn them. Knowing this, the pope issued the humane brief of July 20, 1535, in which every one, on pain of excommunication, was forbidden to hinder the emigration of the Maranos. Soon after the issue of this brief the pope made a proposition to King John—it is said on the advice of Diogo Rodriguez Pinto—to grant pardon to all Neo-Christians, even to those imprisoned, and to permit them to leave the country within a year. In case he did this, the pope would permit the king to introduce the Inquisition in the way he desired. John, however, would listen to no concessions of this sort.
Bull of Oct. 12, 1535.
Tired of these endless negotiations, Paul issued (Oct. 12, 1535) a new and decisive bull, similar to the "Bulle de Perdon" of April 7, 1533, in which he suppressed all suits brought against the Neo-Christians, canceled every confiscation of their property, and annulled all sentences against them without regard to place of residence or to any avowals made by them. In short, he declared all Neo-Christians of Portugal to be free. This bull was published in all parts of the country, the king being unable to prevent it. The whole Christian population of Portugal feared the anger of Rome. John, and still more eagerly the Infante Affonso, hastened to liberate the imprisoned Maranos, especially those who had a recommendation from Rome ("Bullar. Roman." ed. Cherubim, i. 712 et seq.; Herculano, "Da Origem . . . da lnquisição," ii. 143 et seq.). .. The hatred of the king toward the Maranos and his greed were too great to permit him to assent to any such conditions. In order to attain his end he turned to his brother-in-law, Emperor Charles V., to secure his intervention with the pope. Accordingly, when Charles entered Rome (April, 1536) as victor over the Turks, he asked the pope as a special favor to grant John's demand. Paul, however, refused, saying that the Maranos of Portugal, who had been forcibly baptized, could not be regarded as Christians.
Firstly, Tzfat, the Jewish Encyclopedia puts a balanced view — it was bad, it was against converts only and yet they put it in perspective of those times