It all depends on why European powers are there for in first place.
Spanish presence was basically for gold, but as well (and probably more) for lands (in a late feudal perspective), especially in Mexico and religion (in the continuity of Reconquista).
This was difficultly compatible with "natives' right" even if you did have tenatives for that, sometimes successful (as in Paraguay).
French presence, on the other hand, was a bit different. While still dependent on land (as in Canada's seigneuries and Carribean holdings), it was made in a different historical context : religious expansion didn't looked that urging (you had some half-assed tentatives, but nothing that convinced) and colonist pressure far less important.
Giving the differences there, not only more peaceful relations with natives was made possible, but was necessary, as to counter English/British influence and to make the colonies viables economically.
At this point the automatic naturalisation of converted Indians as French was as well reflecting a whishful thinking ("Well, we live with them, they christianized, so they are more or less French isn't, and Canada looks stronger on paper anyway.") than a political objective ("No seriously, we need to be stronger, and not only on paper").
On Carribean, the sugar production was simply what made colonial policy of France in Americas worthwhile, so colonist and slaveholding producers grew more and more autonomous in spite of tentatives on political regulations.
English presence wasn't that distinct from French one at first, the exchanges between populations are importants (as well Europeans deciding that, fuck this shit, they were going native), while charter companies implied these had to be productive; and the growing autonomy of colonies (not only in Carribeans there, but as well on North America, that may be an important difference) with more disagreements between colonists.
All of that eventually exercizing a growing demographical and social pressure that Britain itself wasn't too keen authorizing (but couldn't much about it).
In order to modify colonial beahvior, you'd need to change more or less radically what colonists and therefore the "motherlands" vision of their world. For Spain, it could be arguably to remove the Reconquista part of their identity (meaning at least a VIIIth POD).
Basically it's possible, but you'd need to reshape Europe with a quite early PoD, to find alternatives elsewhere for the more "pressing" needs (basically : someone else is gonna pay).