A rapist deserving such a fate has nothing to do with the issue. Telling Saeko that could have only made the matters worse because Saeko seems like an intelligent person and might have spotted such empty platitudes.

The core issue was that to her dismay Saeko found she likes violence and thus ended up considering herself dirty and unworthy of any man (any decent man worth loving). What better way to show her that's not true than loving her?

I don't think Komuro has the wits to ever become half a quantum physicist but following his dick might have been the best choice even logically.