It is the way they are depicted.
There is a long history of depicting Africans, in film, media, etc. as, at best "the uncivilized other", if not outright caricatured savages. It is not what they are doing, necessarily. It is the way it is presented, in which "they" are implied to be uncivilized. Lesser. Other. Obviously unsophisticated with their "primitive" weapons. Caricatured. And, naturally, one of the only examples of African American representation in the park attractions.
Adventureland in general is very much depicted through a colonizers lens. Not necessarily an American colonizer's lens, but definitely through the lens of an Imperialist country. In that context, it becomes easy to read Jungle Cruise as something of a tour done by the conquering Imperial nation that has "civilized" the river, and the natives being but one obstacle to impede that. They are the only non-animal obstacle on the Jungle Cruise, and they are depicted in a way that is very much caricatured. Unfortunate Implications.
The film on which Jungle Cruise was loosely inspired, The African Queen, likewise takes place in colonized Africa in which the villagers are, at best, an obstacle to the colonizing Europeans.
Jungle Cruise, while far from the worst depiction in any media of such a trope, is not exactly flattering to the villagers either.
And lest this be misconstrued, I'm not calling for them to torch Adventureland or Jungle Cruise. Far from it. But it's not exactly hard to read Jungle Cruise that way.
Fortunately, there's nothing that needs to be done with the actual scene other than a minor redesign of the characters. Nothing more, nothing less, and the gags still work as intended. Particularly since, as you said, it is only a handful of figures in the attraction, none of which were exactly state of the art or particularly iconic as individual characters, save Trader Sam, who will still be there but will just look a bit different, presumably. Everyone wins. It's not as if AA figures have never been redesigned before.
And it's still not quite the same as Frozen. Is it respectful to put a Disney princess film in a pavilion that is not actually the same setting as the film? Not particularly. But there is also not hundreds of years worth of demeaning depictions of Norwegians in media either. That's the difference.
We don't yet know for sure that Splash will not allow fans a last ride. It's been open in Florida since MK reopened.
Their Jungle Cruise is still open too, for the time being.
Anyway, I don't feel like this is going to be that sustantive of a change. It's hardly the first time Jungle Cruise has been updated. If the basic experience of going along the river with your skipper, bad jokes, seeing animals, and things going wrong remains, what is truly being lost? A handful of AA's? Maybe one of which has a face that is iconic in any way?