The bodies of the victim were either burned or covered with a layer of lime, which serves as a disinfectant.
Photo 1: Site of bonfire with human remains.
Photo 2: Kilns were built in order to create enough lime for all the victims.
It was most likely smallpox or measles that wreaked this kind of devastation (meaningful side-eye to the anti-vaxxers).
Check out the full gallery at LiveScience for more pictures and details of the site.