He's not thwarting any prophecy IF he successfully turns Anakin permanently. Anakin was never named in the prophecy, or else you'd think Qui-Gon would mention that. The prophecy likely says that someone will come along and do A, B and C. If Palpatine prevents A, B and C from happening, he is not thwarting the prophecy. He is merely showing that the prophecy has not come to pass YET. If there were a prophecy written in a holy book that says that a messiah will come and unite all the religions of the world under one banner and people started to think that I am that messiah, but then I get assassinated. Does that mean the prophecy was thwarted? No. It just means that they were incorrect in assuming I was the messiah to begin with. If Anakin were turned permanently, all that would prove is that he is not the Chosen One. There was the possibility that the individual that Qui-Gon thought was the Chosen One was not really the Chosen One. There was no guarantee that they had it right, though ultimately they did since Anakin did destroy the Sith.