Threads like this do a fantastic job of convincing me people on the internet understand "innocent until proven guilty" even less than they do freedom of speech (and they constantly abuse that later concept).
At its heart, presumption of innocence is a legal principle. It's found some (limited) application outside that, but at its heart it's about the law. And its fundamental application in criminal courts
The principle often get quoted in threads such as this in a "people should not have to suffer any of the potential consequences of allegations made against until they're proven (beyond doubt)" sort of way. EG, "we should not accuse rapists publically because people will view them as (potential) rapist, and treat them differently as a result of the accusations."
But even the criminal system where the principle originate won't wait until guilt is proven beyond doubt before metting out consequences to accusations. One may be arrested, jailed, and even kept in prison for months if not years without guilt being proven beyond doubt. One will certainly have the allegations against them made public, as well as the evidence against them in most cases, without guilt being proven beyond doubt.
There is no right to not having allegations made against you (beyond libel/slander limitations, which are themselves restricted by free speech. There is no right to not suffering loss of reputation from these allegations (again, with the exclusion of libel/slander law).
Moreover, innocent until proven otherwise, as it exists, exists purely in the court of criminal law, where there is only one party whose guilt or innocence is in question, and where the victim's life and freedom are not at stake. It pointedly does not find application in civil procedure, because civil procedure is not about finding the defendant guilty or innocent, but generally about deciding which of two parties should bear the burden of a given fault. It's for this reason (as well as the resulting difference in the burden of proof) that in many jurisdiction a criminal court's decision is not binding on a civil judge.
The "court of public opinion" is not a criminal court. The court of public opinion does not deal with the life and freedom of one accused, but with the reputation of both the accused and the accuser. And while a reputation of potential rapist may have more consequences than a reputation for making false claims of rape, both are profoundly harmful, so neither should be given lightly.
In short, the presumption of innocence under no circumstances justify the notion that rape allegations should not be made public ; it doesn't justify treating the allegations as false either. It could arguably justify not referring to the accused as guilty or a rapist until they've been found so, but that's about as far as it find application.
Yes, being falsely accused of rape blows. So does being falsely accused of lying about being raped. Both of them will absolutely have people who remember your name looking at you nastily and not trusting you for years and years.
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(As to the case at hand: having not read, and having no intention to read the actual RS article because I find what I have found of their conduct to be awful, I can't say to what extent the original article was a presumption of innocence issue, though the decision not to contact the assaulters does raise question marks in terms of journalistic ethics.
I'm given to understand that evidence has surfaced that call elements of her testimony in question. Reporting on the issues that surfaced with her testimony and the answers of the fraternity involved would have been legitimate ; a retraction calling her untrustworthy is a naked attempt to throw her to the wolves to cover their own mistakes.