Logical Solution:

I grew up in the West. On my way to school each day I passed a small cemetery with poplar fence-post grave markers with cross-members either skewed by time and neglect, or rotted off. 

No evidence at all of who they were. It was said they were from the cattle ranching culture that gave way to farms.

When I migrated to Toronto, I noticed small cenotaphs with grave markers grouped around in tight circles. They marked the old cemeteries that got in the way of new highway traffic ramps. The markers were tightly grouped to mark the site within the space available. I did not dare ask what they did with the bones.

Hey, what a neat way to cover up for the progress of urbanization, I thought.

So, how difficult would it be for people concerned with those evil Indian schools to go and get the names of the children at each site who did not make it through the plagues and pandemics? 

They could be chiselled on a slate or granite slab and mounted in full view on each site. They could even be done like the petroglyphs, uniquely representative of native cultures.

Such memorials could be more appropriate than the few markers afforded for the kids, both aboriginal and immigrant, who died at home over the same period and of the same causes.

Their mostly anonymous remains populate the old cemeteries all across the land.