If the ECHR rules that Knox's human rights (specifically the right to counsel and the right to a fair trial) were significantly breached, then it will do two things: it will order Italy to compensate Knox, and it will order Italy to apply a full remedy. And in respect of the latter, if the ECHR rules that the HR breaches around the various Knox statements from 6th November 2007 are sufficiently serious (as I suspect they will do), then the ECHR will effectively be ordering Italy to annul the criminal slander conviction. That's because the only practical alternative for Italy in that scenario would be to quash the original conviction and conduct a retrial, but with the exclusion of Knox's statements - which themselves are the sole basis for the conviction!
As you point out, one of the more interesting factors could be around whether Italy complies with any ECHR remedy order, or whether it digs its heels in. If it does the latter, it risks being struck out as a signatory to the Convention, which would have far-reaching ramifications for Italy. Normally, countries only take on ECHR rulings where there are general principles at stake (for example, there's one on the table here in UK at the moment over giving prisoners the right to vote in elections). For that reason, I suspect that Italy would be better off quietly complying with any ECHR directives, and annulling Knox's conviction.
If I were being asked to bet on an outcome, I'd say that IMO the best bet is on the ECHR issuing a pretty damning judgement, pointing out the serious, systematic and choreographed breaches of the law and of Knox's human rights on that fateful night. I think the report will call out such things as the deliberate and planned (and HR-breaching) sleight-of-hand whereby Knox was treated formally as a "person of interest" long after the point when she should, by any reasonable measure, have been being treated as a criminal suspect - and thus informed of and afforded the appropriate rights. I think the report will call out the improper (and HR-breaching) way in which Knox was interrogated that night, from moments after she entered the interrogation room, right through to Mignini's trick of getting Knox to make a "spontaneous declaration" with the deliberate intent of manipulating the law/code to obtain a statement that would be usable in court. I think the report will call out the wholly-inappropriate and improper role played by the police's interpreter. I think the report will call out the grossly improper (and HR-breaching) manipulation of the law by Mignini in denying Knox access to a lawyer until literally moments before her court arraignment. And I think the report will call out the shockingly improper (and HR-breaching) way in which her criminal slander trial was conducted in parallel with the murder trials, thus giving an improper reinforcement loop to each (i.e. "Knox admitted she was there and falsely accused Lumumba, thus Knox participated in the murder - and if Knox participated in the murder, this is the obvious proof of her motivation to falsely accuse Lumumba....").
And I think that Italy will indeed quietly comply with the ECHR directives, and will quietly strike off her criminal slander conviction. We'll see.