Complex sentence: The rationale is that Jews would adopt as family name an (apparently) Christian concept as a deception: in fact they were choosing the most incorporeal Trinity person, that is, the one that offended less their (secret) Jewish faith.
Split into simpler sentences: The rationale is that Jews would adopt as a family name an (apparently) Christian concept as a deception. In fact, they were choosing the most incorporeal Trinity person, that is, the one that offended least their (secret) Jewish faith.