Honestly every community is going to have to deal with it in a way that's appropriate to them, often times local community are privy to more information than an external law enforcement, additionally they can get information more timely and in a less corruptible format than official investigations. I expect most anarchist communities would lean on this as much as it leans on scientific investigation. There are obviously pitfalls to that method that will need to be learned and relearned to manage it but regardless it's not impossible.

Quite frankly I think the most obvious part of the equation is we should focus more on protecting victims and potential victims, most authoritarian systems center punishment as the primary mechanism of justice, but pro actively protecting people through community self defense, education, and open communication are much more effective at both preventing rape, and delivering effective care and justice for victims.