its possible that rather than using the tool we have to stop threats to town we're meant to try to guess what might trigger an individual's transformation and then avoid that. Storm said that for him it was completely random, which coincides with what happened in the comic, though what zinger said implied we could have stopped it. Its possible arresting him would have stopped him from working on power lines and thus receiving the big zap.
the wiki says that kingpin was basically born a villain, and was called "the king pin of crime" by the time he was 15. Our fisk is probably already an adult, and should thus canonically already be the kingpin. I'm not really seeing anything like an origin story for him, so i don't know how you'd stop him from turning to crime or whatever, which means if we want to deal with him we might have to fall back on arrest.
IIRC kraven becomes kraven when he drinks a jungle potion he received from some african tribe (sounds pretty racist to me), and so in theory just preventing kravinoff from taking actions could prevent that from happening, which makes arrest viable. Other than that, maybe figuring out how the jungle potion could be made or obtained using information roles like the bugle and preventing that from happening is also an option, though a more nebulous one than simply arresting CL.