An idea, is that you can get the colony to be really nativists against immigration, and that it actually tries to preserve it's deals with the Natives. Like not encroaching into their land, but continuously trading with them, which allows the Natives to recover their numbers as they use the arable land in the Midwest for agriculture. Eventually, the Natives would be invited to join the confederation that the colonies have which would allow free movement into the united land and invite for more exchange in culture and ideas which they already were having before. Remember the Americans frequently massacred the Natives and kept doing that would prevent their population from recovering such as the trail of tears and all of the forcing them to the west.
A lot of the surviving American Indian groups weren't really incorporable into a Euroamerican-style state, though, like basically any Plains Indian group that relied on the buffalo hunt. Their interests were diametrically opposed to those of the European settlers, and the European settlers had a lot more force on their side.
Even with the agricultural Indians, they'd have to significantly change their agricultural practices (which peoples are you referring to), and even then, they'd be like what some wealthy members of the Five Civilised Tribes were in the South--indistinguishable from whites but from the colour of their skin and their heritage. And I see many of their neighbours being very jealous of the lands owned by these Indians. The dominant culture considered American Indians a curiosity at best, and generally when in direct contact, an inferior. And demographically, the natives were always at a severe disadvantage, even counting "Native Americans" as a unified group (which they weren't at the time, and the Americans and others knew it and exploited to its fullest extent).
About American massacres, it there any count from American massacres versus those committed by native groups against whites and others? It is obviously a self-sustaining cycle of violence generally comparable to warfare. We also can tell that native population recovered to a degree from epidemics, based on the demographics of the Comanche and Sioux in the 19th century (for the Sioux at least, ironically because of the United States to a certain extent).
By that logic, the Europeans were screwed as soon as the Black Death arrived. Of course there's no way you can prevent diseases from killing LOTS of Natives, but that doesn't meant that the populations have to stay permanently small. What you need to do is to create resilient social structures amongst the Native population which prevents epidemics from causing wars and instability, and instead responds to epidemics with increased birthrates and compassion for those hardest hit.
Europe's population recovered to its pre-Black Death levels within about 100 years of the epidemic (ok, I don't have the numbers in front of me, so I might be remembering the population figures for only one part of Europe rather than Europe as a whole). This was due to high birthrates, amongst other things. If we can get Native people to respond to the epidemics with high birthrates rather than war amongst themselves, then the Native population can also recover.
I guess my point is that the lack of disease resistance amongst the North American Natives was as much cultural as it was biological. Yes, having actually immunity to diseases would have helped, but I feel like the biggest factors preventing a population recovery were social/cultural practices such as 'mourning wars' where deaths (such as those due to disease) would cause the bereaved to go off to war to search for captives to replace lost family members. This social/cultural practices can be changed pretty quickly (especially in times of crisis), although it would require a series of finely tuned events to make them change in the right way at the right time. Really, by quickly I mean within two generations or so. I'm not talking about a complete reversal from one year to the next, but a change which gradually takes place over 50 years or so.
50 years of social change plus 100 years of population recovery can lead to resurgent populations by 1650 or so.
If you get rid of some of the healing practices or alter them, like sweat lodges, you'd change a lot. And also, the Black Death wasn't the first time plague struck Europe--that might've been the Plague of Justinian. Here you have a group separate from Eurasian/African diseases for over 10,000 years minimum being hit by all of them at once. Not just smallpox, but measles and numerous others that will utterly decimate them. The only good thing is, "it could be worse".
Inoculation as a cultural practice might be interesting but semi-ASB--seems like it require a more organised and more hierarchal society than existed outside of Latin America and possibly the Pacific Northwest.