Much of this is Disney's own doing. Pirates are the good guys in their pirate film and television franchises.
See above. I agree with all of your points here, but the main issue is that Disney wants pirates to be seen as protagonists now, instead of the antagonists that they were for nearly 40 years of the attraction's existence.
Once the Pirates movies became a thing, Disney shifted the narrative to be that Pirates are the heroes and are people that kids should want to emulate. We see that in attractions like Pirates League as well, where kids can literally become pirates.
The attraction, as originally designed, was a morality play. The pirates were bad people who did bad things and wound up with a bad fate. Once Disney decided that they wanted to encourage kids to be pirates, the waters got a little muddy and the tides a little stranger.