No: Machiavelli does in fact have a point in this particular instance. One doesn't need to have firm knowledge about who committed a crime in order to make a criminally (in Italian law) slanderous accusation against another regarding the crime.
For example, let's suppose that Mr A lived in Perugia at the time of the murder, and that he had a grudge against his neighbour, Mr B. Suppose that neither Mr A nor Mr B had any involvement in Meredith's murder. But suppose that Mr A was fuelled by his grudge to walk into a police station on the 3rd November and tell the duty officer that Mr B was the murderer. Once it was (hopefully, but you never can tell in Perugia it seems) established that Mr B had nothing to do with the murder, Mr A could - and probably would - be charged with calunnia.
This, in many ways, is the situation that Knox currently finds herself in. Just because she's been acquitted of the murder - even if she has been acquitted on grounds of innocence rather than reasonable doubt - this doesn't mean that she can't have knowingly made a false accusation against Lumumba. In other words, the law treats ignorance of the real perpetrator as equivalent to knowledge of the real perpetrator when it comes to making false accusations. Indeed, there need not even have been a real crime at all. Imagine if tomorrow Mr A walked into a Perugia police station and told the duty officer that he had just seen Mr B punch his wife hard in the face (which would be a criminal act of common assault or worse in most jurisdictions). If the police investigated and found that Mrs B had no marks on her face or any other part of her body that were consistent with punching or other forms of assault, then Mr A could similarly be charged with calunnia.
So - in contrast with the views of many (including, ironically, Machiavelli himself) who assert that the acquittal on the murder charge is incompatible with the Lumumba slander guilty verdict, these two position are actually entirely mutually supportable. Here's why: suppose - probably correctly - that Knox had nothing to do with the murder, and also that she had no accurate knowledge of who the real perpetrator was by the night of November 5th 2007. It's possible that the police were putting under a lot of pressure, and that Knox felt that the police were turning their attention increasingly towards a suspicion of her. So it's entirely possible, that under such circumstances, Knox might have spontaneously decided to "get the police off her back" by making a spurious accusation against Lumumba - when she had no idea whether or not Lumumba was involved. In such a scenario, Knox's accusation of Lumumba would absolutely definitely be a criminal act of slander under Italian law.
However, while I've outlined above the circumstances whereby Knox could factually have committed a criminal slander, I must stress very strongly that I don't believe that this is what actually occurred. I don't think that Knox committed a criminal act as defined in Italian law when she made the accusation against Lumumba: I think she was unlawfully coerced by the police into making the accusation, and that she effectively retracted the accusation within a reasonable period (given that she was under arrest and in police/prison custody from the moment of the first accusation). I don't think that the court can prove the requisite mens rea for the crime. And I also believe that there was a major judicial error when the first trial judge (Massei) ruled that the calunnia charge could be tried concurrent with the murder charge. I think that if Knox appeals the calunnia verdict, she will very possibly get a retrial on this charge, and that she may then very possibly get an acquittal in the retrial.