One thing I might ask though is how many people were actually offended by the song itself before they were told that they should be offended by it? That's not to excuse it's origins, but can it exist beyond that if people want to let it or to think of it a different way. I'm not claiming to answer that as obviously the answer will be different for everybody, but I think that's one aspect to think about.
Truthfully, I don't know. I certainly never personally thought of it or even Splash as offensive or disparaging, but I've heard some characterize it that way. And I still don't feel like it was really my place to be the arbiter of that. For me, racism was something I learned about, not experienced, so I'm not sure I'm the right person to gage what is truly offensive on that front. That doesn't mean my voice or opinion doesn't matter, but I admit my blindspots (instead of reacting defensively, for example) and make a personal choice to be a little more deferential as a result of those blindspots.
The way I look at it: my lack of knowledge of the song's "offensiveness" doesn't nullify its potential to make some Guests feel uncomfortable. It's quite possible (and even likely) that those Guests might be expressing that discomfort is circles that I do not frequent. Most of those Guests likely don't have the same sentimental attachment to the song that you or I or many on these forums do. Likewise, I think we have this tendency (especially on the internet) to speak in extremes and get defensive. "It's offensive." "It's canceled." It could also be that the song made certain Guests feel uncomfortable or perhaps evoked a certain cultural context that was painful. I would imagine Disney -- with enormous resources at its disposal -- is far more in tune with those conversations than I am. Given the money they make on Splash merchandise and the concerted effort required to explicitly remove Zip-a-Dee-Doo-Dah from soundtracks across the parks, I cannot imagine they rushed this decision, acted rashly, or allowed themselves to be pressured into something they didn't deem necessary.
To answer your secondary question, though there are certainly different nuances, I think the same could be said about the Confederate flag: disregarding its origins, can it exist beyond those origins? To one group of people, it can, but to another group (who were caught in the crossfires of those origins), it cannot. What do you do? My belief -- and certainly some cynic (on a Disney message board no less) will come along and tell me how wrong and foolish I am -- is that you lower your defenses, assume best intentions, and have a conversation to try determine what elements of it make it hurtful. How do those origins manifest in its current form? Nobody's ever going to have the definitive answer to "is that offensive?" but I think more people should be willing to listen and not view every concession of something being out of date as an admission of personal racism or immorality. I think if more people went into a dialogue like this one with a more open-mind and a less defensive attitude, it would be easier to figure out where that line should be drawn. In the meantime, Disney drew the line (and they reached that decision likely with a lot more information and research than you or I have at our immediate disposal).