What is the proper way to apologize for smearing rape victims?
By apologizing. Sorry, but that's all he can do.
But that's not my point. Last I heard of the case, the girls never pressed charges against him. They merely wanted to have him tested for VD. The prosecutor pressed charges (as they must do under Swedish law) when she (because I think it was a she?) heard their story.
The prosecutor thinks there is a rape case here. Whether a rape has actually taken place is now up to the courts (since the girls themselves have not wanted to press charges for rape we can't really say there was a rape at all until that has been established in court).
This system is in place to prevent the very thing you describe above, that in a lot of cases victims are shocked or threatened into silence so in those cases if the police (the prosecutor) thinks he/she has enough to make a case, they must press charges.