Now, again, Lucas may have intended for the prophecy to be Anakin defeating the Sith, but what was intended never made it on film
It made it on film in two places in ROTS. It wasn't thrown out by their speculation in one of those places about whether the prophecy was misread, because that was about whether or not Anakin was the Chosen One, not what the Chosen One was supposed to do, and anyone who had seen ROTJ knew that the Jedi doubt on that issue would ultimately not be supported by events, so the prophecy was actually not misread in the sense suggested. In fact, anyone who had seen ROTJ should have guessed what "bringing balance to the Force" meant without being told by ROTS, just from knowing in advance about Anakin's final actions.
If the prophecy point blank said "The Chosen One will destroy the Sith," (which sounds pretty cut and dry), why would Yoda say that they may have misread it? At that point in the story, there was no indication that Sith were going to win. If anything, it seemed as if the Jedi were going to come out on top. Yes, viewers might know what happens, but that doesn't explain away the poor character actions.
Personally, I think the prophecy says something that is vague that the Jedi interpreted as "Destroying the Sith". Bringing balance to the Force seems the be the driving force behind it. However, this can mean a number of things. In TPM, all Mace says about it is that the Chosen One will bring balance to the Force. He doesn't say squat about Sith. Since the Sith just came out of hiding in TPM, the Jedi would logically (and ultimately correctly) assume the emergence of the Chosen One would be the one who destroys them.
This actually makes sense in context with Yoda's wondering if they misread it, which would make the whole fall of the Jedi more interesting and increase the value in the prophecy within the prequels instead of making seem throwaway.
Thing is, and this has been my point, is that we don't know what the prophecy says, how detailed it gets, or its overall importance. It has only been alluded to, leaving it up the the viewer to try to figure things out, but things don't completely add up and just opens up more cans of worms when trying to explain it in context to everything else that happens.