“I was thinking the bodies could also include local Indians”
Only if they had converted to Christianity......
The burial ground was considered consecrated soil.....
I doubt they would have been in St. Augustine otherwise. The Spanish had set up a series of missions in Florida most of which were inhabited by local Indians. These missions have been the subject of some recent archeology. If I recall correctly the English drove most of the natives out and handed over the land to their allies the Seminoles.