The biggest issue with adding the film characters into the ride is that it recast the pirates as heroes. The original version of the ride had the pirates as villains, and the ride functioned essentially as a morality play.
Once you add sympathetic characters from the film to the ride, the pirates are no longer seen in a dangerous light.
You raise a critical point here. The addition of the charismatic and heroic Jack Sparrow altered the context for all the pre-existing pirate pillaging. But it's complicated.
I don't 100% agree that the original iteration of the attraction presented a clear morality tale. I'd like this to be the case, as the pieces of the morality tale are all there and I generally view the attraction in that light, but I don't know that this assertion holds up under scrutiny. Yo Ho is just too catchy and lovable. The trio of singing pirates and the dog and donkey barking and bopping along are just too adorable. The auction scene is a (dark) joke just as much as it's a historical depiction of pirate violence (they want the
redhead, not the heavy-set woman! Haha!). And the audience is meant to chuckle, not recoil, when the naked woman appears in the barrel behind the pooped pirate. I'm not saying the original attraction was reprehensible or anything (see: my avatar), but I think it's a bit of a grey area how exactly the audience is supposed to feel about the pirates.
That said, I've never understood how any rational adult can sincerely believe the actions of the pirates on this attraction are
intended to be heroic. As if invading and burning a town, torturing men, and auctioning off women was totally cool in 1967. Back in 2018, when Disney added the Redd/hen auction scene, it seemed so dishonest and bewildering to me when advocates of the changes would say "Now,
finally, little girls riding the attraction have a role model to look up to, as well!" As if boys experiencing the attraction look up to all the dirty pirates with teeth missing, dressed in ragged clothing, who are shown to be repulsive to the women of the town.