It's worth pointing out that the abstract of the Nature article appears to suggest that the pre-Columbian evidence is for a different variant of TB: "Here we present three 1,000-year-old mycobacterial genomes from Peruvian human skeletons, revealing that a member of the M. tuberculosis complex caused human disease before contact. The ancient strains are distinct from known human-adapted forms and are most closely related to those adapted to seals and sea lions."

This is completely speculative, but if post-contact TB was a different strain imported from Europe, that may explain why it took such a toll on Indigenous peoples.