You're not starting with much - by 1871 there are census documents giving you 102,000 natives in Canada or thereabouts, but who knows how accurate they are? You also still have pressure from colonists from Ontario moving westward. You could have Riel do better, but Métis and natives will always have to deal with the challenge of fighting a better-armed, more organized group of conquerors. Even if you get a more secure Manitoba, eventually Europeans will look at the province as an attractive place for farming and start heading west.
Even before 1860, there was a mindset deeply entrenched in Canada that it was the right thing to do to administer First Nations peoples in such a way that they would be compelled to become enfranchised - that is, Europeanized, giving up their Indian identity. Residential schools were already getting their earliest iterations going before Confederation, too.
You could always have John A. Macdonald lose the 1867 election, but there's not really much hope for getting someone "pro-First Nations" at that point. Maybe a hypothetical Prime Minister George Brown is too busy ranting about "French Catholic priestcraft" and the Irish for a real systemic action against First Nations - the Catholic Church did administer a majority of the residential schools, as far as I know, and maybe Brown sees their presence in the west as unacceptable. That said, I don't know that he'd be any more mild towards First Nations than John A would've been.