The first order of business would be to ask the priest you heard to substantiate his claim that Protestant clergy and laity of the time believed that African slaves had no souls and thus heckled Catholic priests who believed otherwise. While I have indeed heard that Catholic priests would baptize the African slaves before the start of their deportation to the New World, the claim about Protestant clergy and sailors is new to me. Given that the Catholic priests were usually accompanying Spanish and Portuguese slave traders who came from Catholic, not Protestant, countries, it is incomprehensible that the priests would have been heckled by Protestants in the course of their ministry.
This isn’t to say that Protestants were not involved in the slave trade. Indeed, John Newton, author of the song “Amazing Grace,” was a slave trader before his conversion to Anglicanism. It also isn’t to say that some Protestants didn’t have racist ideas about Africans. The Protestant minister, Cotton Mather, as one example, believed in racial spiritual equality but taught black slaves that their submission to their white masters was a positive spiritual duty (
source).
But these views are not all that different from the general belief of Europeans, Catholic and Protestant, toward those of other races. It was a common failing of Europeans to treat blacks – and American Indians – as inferior to themselves. The difference between Catholicism and Protestantism is that the Holy Spirit protects his Church from infallibly defining doctrinal or moral error, and that the Church had the fullness of revelation at its disposal in understanding the racial problems that arose with the exploration and settlement of the New World.
In short, while the priest could have made a sound argument that the Church was protected from making doctrinal or moral error in addressing racial relations in the Age of Exploration, he should not have tried to score points against Protestantism by pointing to the moral failings of its adherents. Just as we would like Protestants to consider the Catholic Church on the merits of its history, theology, and the lives of its saints, so it is only just to do the same for Protestantism.