I think it's wrong to judge the standards of one epoch by the standards of another but though some of H. Rider Haggard's terminology may be slightly cringe-inducing it is as you say. He genuinely respects and admires African (especially Zulu) tribal culture & actively encourages his readers to do likewise.
Interestingly, Quartermain has enjoyed a minor revival of late due to his cult status among Steampunks. They tend to be very quick to label people & concepts as racist but it's a charge which is very rarely made against Haggard.