I don't see Macdonald saying he wants to ethnically cleanse them. That means to remove natives physically from Canada. His actions were essentially what we now call cultural genocide, for the supposed sake of their education/welfare. He wanted to remove all Indian culture from the kids because he saw the parents and their native culture and way of life as savage. This went on in many European colonies throughout the world, the "white man's burden" to "save" the heathen savages, many times led by Christian churches/missionaries.
Clearly many of the schools were run by racists and/or cruel people who didn't care much about their physical welfare either. Macdonald was very likely a racist himself given his comments.
I think it’s worse than that…. You’re white-washing how the country was founded, and stolen, from natives who were seen as subhuman.
It’s not as simple as saying that the founding of Canada was great but he also did bad things.
The founding of Canada was done in a terrible and atrocious manner. Until Canadians can reconcile that fact, I think good relations with indigenous communities will likely not be possible.