In his own mind, did he mean well?

Pratt was against racism. 

"Association of races and classes is necessary to destroy racism and classism."

~ Richard Henry Pratt

So he was an anti-racist who wanted everyone to be aligned with the dominant culture, whatever that was?

"The Ugly, Fascinating History Of The Word 'Racism'": Code Switch : NPR

https://www.npr.org/sections/codeswitch/2014/01/05/260006815/the-ugly-fascinating-history-of-the-word-racism