The thing that puzzles me here is why Knox was ever prosecuted at all. The prosecution had Guede.
The answer is simple and banal: they didn't get Guede until after they had already decided Knox and Sollecito were guilty. Not prosecuting Knox and Sollecito would have required them not only revise to previous beliefs in which they had become psychologically invested, but also to retract previous public pronouncements -- in short, to admit they had been wrong.
From the inside of their minds, no doubt, Knox and Sollecito just felt so suspicious, in the early days of the case before the physical evidence came in and they were relying on behavior to form hypotheses . It's also likely that they were irrationally angry at Knox because of the false implication of Patrick Lumumba that they coerced out of her, and that this anger and frustration at the failure of their own hypothesis morphed into a sense that Knox was an evil vixen.
I think you skip some details. Sollecito withdrew his alibi for Knox. Then Knox implicated Lumumba. And they really go after the guy. Interestingly they fail to railroad Lumumba in the way in which you think they railroaded Knox. Which to me is really interesting because it doesn't fit the 'evil police' story.
Knox of course claims it was extremely coercive, took hours, and some physical abuse from the police. Police denies abuse. We can't really tell either way, but prosecution ought to know how coercive they were. So that's another opportunity to really p...
Here are the New York Times, CNN, and NBC. Here is Wikipedia for background.
The case has made several appearances on LessWrong; examples include: