I don't buy the implicit (explicit?) argument of the title for a second. Beauty comes with many advantages; show that in all of Italy, beauty's advantages were overall negated and became a disadvantage - that the ugly were favored - and then I might buy that Knox's looks actually contributed to her persecution. As it is, it looks like the fix was in well before the media storm that one might argue continued the persecution.
Two offhand links about the advantages:
Charles Petzold writes about Nina Burleigh's "The Fatal Gift of Beauty: The Trials of Amanda Knox".