Actually if you go "back to John A's times and the start of those schools", natives (or at least those on the Prairies) were actually interested in learning "the white man's ways" for such things farming as they realized the buffalo (at least in the U.S.) had been slaughtered and their old nomadic life was disappearing. 

Of course the Residential School System as it ended up cannot be defended. A lot of that I'd suggest would be because the parents and students had absolutely no say in how it was run. (Note that there are other examples of schools that were also quite bad, e.g. Mount Cashel Orphanage, where there was little oversight as to what the teachers did.) 

As to whether or not the original system was as bad as it ended up being, I don't know.