Because pirates tend to do pirate things...Even if you want to make a story grounded in "PC" culture, it still needs to have some grounding in reality, or people will start to be pulled from the immersion of the story. Part of the reason why Pirates works, is because the immersion of the story is all consuming. The pirates are silly, but the story is about what pirates do. They are crass, they are violent and they do bad things. Up until the 90s, the pirates still stayed within a general rue of being pirates, with a story that showed them as less than scary.
With the changes...Jack/pirates being chased off by brooms/etc...the pirates look less and less like, well....pirates. They are falling more and more to the cartoon side and less and less recognizable as a threatening group of plunderers. The narrative has switched from "Look at pirates doing bad things in a fun way" to "Look at pirates not really acting like pirates".
Small changes can affect the immersion of the attraction and detract from the story. Those small changes have a massive impact on the feel of the attraction. While the overall impact of one scene may be small, the cumulative impact of the edits has left the artistic vision of the ride drastically altered.