Given that the accuser accepted Franken's apology, I don't see the problem. The way you're describing it is less punishing him for what HE did and more making an example of him for the injustices leveled against victims EVERYWHERE. And that seems WILDLY unfair.
I mean, you're fine with exonerating him in order to incentivize other people to confess, but like... the point of a confession is typically to accept a punishment. If you're not punished, a confession is just gloating. Yeah, I'd rather make an example of him than that, and I think resignation is a fair punishment that still makes an example of him.
An apology and actively calling for an investigation into your own potential wrongdoing seems fair at this point in time, rather than immediately treating him on the same level as Anthony Weiner. ---