I share others' view that this is less about seeing the biggest culprits (especially Stefanoni, Mignini, most of the Perugia Flying Squad) punished per se. Rather, to me it's about a) seeing those people properly held to account, and b) taking all proper steps to minimise the chances of this sort of thing happening again.
So I think Stefanoni should be subjected to an investigation, and (after due process) removed from the forensic science community. I think Mignini should be investigated by the appropriate body, and (after due process) removed from his position of authority and formally censured over his conduct in this case. I think that most of the Perugia Flying Squad should face disciplinary investigations.
But on top of that, I think that certain structural changes need to happen, to try to minimise the chances of this happening again. Firstly, the police and courts need to get a grip on low-template DNA evidence, and put all the crucial protocols and processes into place. Secondly, the (seemingly ad hoc) practice of sending lab technicians out to process crime scenes should be formally forbidden. Italy must make sure that specialised crime scene investigators are trained and available for this sort of work. Thirdly, I think that the top brass of the Italian judiciary - probably the Constitutional Court - need to sort out the institutionalised problem of the improper relationship between trial judges and prosecutors. They need to ensure that the adversarial system is rigorously enforced, that there is full and open discovery to the defence, that defendants truly ARE treated by the courts as innocent until/unless proved guilty beyond a reasonable doubt. And lastly, I think Italian legislators urgently need to draft new laws concerning police/PM practices during an investigation - something similar to the UK's PACE act.