I agree that the prophecy’s primary function in the story should have been a criticism (if not an outright condemnation) of the Jedi Order’s myopia.
On a metatextual level, we all 100% know the Chosen One prophecy was just Lucas taking the easiest storytelling route possible to make Anakin “special” in a way that further retconned the end of Return of the Jedi to be Anakin’s ultimate triumph, not Luke’s. But in the text, it could have been (and should have been) used as a means to show how the Jedi had so disappeared up their own ass and taken their eye off the ball that they never saw Anakin coming. That kind of happens, almost by accident, throughout the Prequel’s story being lurched through over the course of the trilogy. But like most good ideas embedded in the Prequels, its never fully realized, and its potential goes unfulfilled.
However, Palpatine’s returning doesn’t nullify Anakin’s sacrifice, even if it muddies the ultimate “truth” of the Prophecy. I think proving the prophecy to be somewhat bullshit isn’t even a bad thing, honestly. Prophecies suck in general, and are rarely used well in a story. Their best uses come as punchlines to tragic jokes. But Anakin’s sacrifice doesn’t cease to have meaning if Palpatine somehow survived for 30 years. The Sith were still wiped out for all intents and purposes (at least they didn’t wait a millennia before popping their head back up this time) balance to the force was more or less established, and the galaxy sustained a measure of peace for about 30 years. That’s pretty good for Star Wars. Of course, all of that is secondary to Anakin saving his kid, which is the real emotional and storytelling thrust of Return of the Jedi, and that thrust isn’t dulled or cut short by Palpatine’s reappearance in The Rise of Skywalker. Anakin still saved his kid. That hasn’t changed.
It’s always a possibility that Anakin, or his spirit, rather, will still show up at the end of this movie to assist in Palpatine’s final removal from the galaxy. At which point the prophecy is still accurate.