I came across this hilarious parody site as I was writing this post. They have an explanation as to why the bride wenches were left in the ride:

One of the original scenes in Pirates showed a number of lascivious scallywags chasing innocent women. The thought of what the pirates would do to the women once they were caught disturbed many guests (some of whom did not realize that the pirates just wanted to sing their jolly song to the ladies). After the 1997 renovation, this scene had been adjusted with a focus changed to pirates stealing food and illegally duplicating video tapes. The scene in which women are being auctioned was not changed — the “Buy a Bride” scene's intent was to show women being sold for marriage, so the “moral majority” was not bothered by it since there was no implication of pirates having premarital relations with their purchases.

I was just at Disneyland a couple months ago and Pirates was shut down for the renovations you mentioned. I assumed that it was to get the ride in line with the new film.

I'm just kidding, of course. I've actually been convinced for some time that the redhead is really a man.

Lovely.

And I think you mean Elizabeth Swann, don't you?