There's nothing truly controversial about Song of the South. I've owned a bootleg copy for years now (given to me, free of charge, by a total stranger, just in case Disney's trolling about) and it's biggest crime is in how utterly boring it is between animated segments.
While Remus' life is portrayed in an inarguably "whitewashed" manner, the film doesn't in any way imply that this is the sort of life enjoyed by every slave. Nor does it imply that slavery is good. It's no more offensive than gone With the Wind, or dozens of other "classic" films with dated or inaccurate historical representations.
If Disney were smart, they'd start production on new Brer Rabbit cartoons. Begin by remaking the original shorts, as shorts, as part of John Lasseter's desire to bring the animated short back to theaters. Leave Uncle Remus and de lil' chilluns out completely, and start rebuilding the Brer mythology among the sorts of people who'd care enough to write negatively about such a project as a lighthearted exploration of how slaves in the real south resisted cruel and unkind masters.
Because the Uncle Remus stories, at day's end, are actually very cool, sometimes sad, inspirational things. They come from the lives of blacks who experienced slavery firsthand. Even if Harris (Uncle Remus' compiler) was racist, the stories are not. They should be celebrated as a positive part of black heritage.
Here's a little bit on the stories. It's Wiki, so it's up for debate as always, but the essential facts are right:
http://en.wikipedia.org/wiki/Uncle_Remus