I think you have slightly misunderstood the issues.
1) The ECHR is considering the question of whether or not Knox's right to a fair trial for callunia was breached in respect of an alleged denial of her procedural rights together with claims under two other articles, one of which, (art 3), if upheld, will also be deemed to have breached her right to a fair trial. So, Knox's essential claim is more than simply a 'breach of her right to a lawyer'; it is that the callunia trial was unfair. The denial of a lawyer was, it is claimed, one of the means by which the police caused the trial to be unfair.
2) If the callunia trial is found unfair as a result of the denial of Knox's right to counsel, then all statements, which were the product not just of a particular interrogation, but of the entire time she was denied counsel will be unusable, contradicting the Gemelli court. In Salduz v Turkey, the court held that .."the restriction [of counsel] should not unduly prejudice the rights of the defence, which would be the case
where incriminating statements made during a police interview without access to a lawyer were used as a basis for a conviction." In Zaichenko v Russia, the court stated: "Bearing in mind the concept of fairness in Article 6, the Court considers that the right not to incriminate oneself cannot reasonably be confined to statements of admission of wrongdoing or to remarks which are directly incriminating....
Testimony obtained under compulsion which appears on its face to be of a non-incriminating nature - such as exculpatory remarks or mere information on questions of fact - may later be deployed in criminal proceedings in support of the prosecution case, for example to contradict or cast doubt upon other statements of the accused or evidence given by him during the trial or to otherwise undermine his credibility."
3) If the callunia trial is found unfair as a result of a denial of Knox's right to counsel or because of inhuman and degrading treatment, then certain responses by the Committee of Ministers at the Council of Europe and from Italy will be triggered.
4) Whilst the court limits itself to ordering compensation payments or "just satisfaction", yet it is the Committee of Ministers, which is charged with ensuring that "individual measures have been taken to ensure that the violation has ceased and that the injured party is put, as far as possible, in the same situation as that party enjoyed prior to the violation of the Convention". Indeed, the court itself may remark that in its view the re-opening of domestic proceedings is the most suitable method available to Italy for remedying the breach of Knox's rights under the convention following the principle of restituto in integrum. But it will not order or even recommend a retrial; indeed, as you point out, a retrial is not possible: "The European Court is...badly placed to make such an assessment, which presupposes a relatively detailed knowledge of the domestic order in question". And: "...it is for the competent authorities of the respondent State to decide what measures are most appropriate to achieve restitutio in integrum, taking into account the means available under the national legal system. Bearing in mind, however, that the practice of the Committee of Ministers in supervising the execution of the Court’s judgments shows that in exceptional circumstances the re-examination of a case or a reopening of proceedings has proved the most efficient, if not the only, means of achieving restitutio in integrum."
http://www.echr.coe.int/LibraryDocs/DG2/HRFILES/DG2-EN-HRFILES-19(2002).pdf
5) Italy has already determined that no guilty verdict can survive a finding of a violation of Article 6 and so proceedings will indeed be re-opened. The verdict will be vacated according to Italian law. However, since no evidence against Knox will remain and because the statute of limitations will ensure that no further trial can take place, the charge will be dropped and she will have been acquitted. The civil case will similarly be dispensed with as the judgement here will also be vacated. Lumumba's remedy is to pursue a claim against Italy, to the extent he is able to do so.
6) It would appear that a friendly settlement would not permit the reopening of domestic proceedings since a judgement by the ECHR is predicated on it. (A finding of an Article 6 violation).