The privilege to whitewash the history of this period, presenting it as a happy-go-lucky time when we all got along and yearned for the old days, has everything to do with why some feel the movie, and by extension the ride, are racist.
As to the rest of your post, I understand exactly what you mean. Of course a fictional movie is not "about reality." I don't think all "problematic" art should just be washed away, and I actually think Disney could've avoided a lot of this trouble had SotS been "out of the vault" and demystified over the years. I've watched dozens of movies from the 20s, 30s, 40s, 50, 60s, etc. I understand that they're in part expressions of values we no longer hold. I believe that they have considerable value beyond that. I wish, genuinely, that I could show the world some of these films and talk about them. I think they're amazing, both at the surface and unpacked, in different ways.
However, the cat having been let out of the bag, as it were, perhaps you can understand why many feel a theme park is not an appropriate catalyst for some of these discussions, that bad feelings would out in too many cases, etc. If anything, I would've preferred a small contextualization of some kind, like the one I understand HBO is inserting at the beginning of "Gone with the Wind." That could have been fair middle ground to please most people, since the ride is pretty divorced from the film, but perhaps Disney was thinking of threads like this when they considered the potential for extreme reactions on either side to any change or acknowledgment.
