The book I quoted says:
As Capuchins and apostolic missionaries, they asserted, they were amenable only to the Roman authorities. And they continued to preach against Negro slavery.
I don’t think they had any sort of special papal exemption due to corruption or anything like that. They thought that their status as missionaries meant that they weren’t subject to the authority of the local bishop.
Its true that the Catholic church came around to oppose slavery, but the shift didn’t become mainstream until a few decades after these excommunications. Earlier objections to slavery were mostly concerned with opposing the enslavement of Christians, for example:
Pius II was opposed to the enslavement of freshly baptized people.
Pope Paul III condemned the enslavement of Native Americans, but withdrew his document very quickly and later allowed enslavement of Muslims.
Urban VIII banned the enslavement of Native Americans living in Jesuit missions.
The later moralists, that is to say, broadly speaking, those who have written since the end of the eighteenth century, though in fundamental agreement with their predecessors, have somewhat shifted the perspective. In possession of the bad historical record of slavery and familiar with a Christian structure of society from which slavery had been eliminated, these later moralists emphasize more than did the older ones the reasons for condemning slavery; and they lay less stress on those in its favour. While they admit that it is not, theoretically speaking at least, contrary to the natural law, they hold that it is hardly compatible with the dignity of personality, and is to be condemned as immoral on account of the evil consequences it almost inevitably leads to.