Exactly. According to Wikipedia they deliberately removed the Uncle Remus character when developing the attraction, so they already were fully aware of how offensive the film yet they developed the theme anyway, seemingly thinking they could get away with just using the animated characters and ignoring the plot?
I presume their thinking was that they could retain all the characters from the cartoons, and remove all the elements from the live-action frame story. The frame story is what garnered most of the complaints about the film.Uh, yeah? Song of the South was wiped from the face of the earth already, this iconic ride serving as a monument to it has always been tone-deaf and puzzling.
Apparently the SOTS characters and Splash Mountain are in the 2011 videogame Kinect: Disneyland Adventures. So even in a more modern era, Disney seems to think they can try to keep the enjoyable elements of the film around and try to sweep the distasteful parts under the rug. The film itself will likely stay locked in the Disney Vault forever, I imagine.