Wolf -“But the point is this: if machnisim oso l’kippah was an option, by would SbS have been so pained? The obvious answer is that it was not an option and that, absent the Divine intervention that ultimately happened, the man would have gotten away with the deed”
Your mistake is machnisim oso l’kippah is Divine intervention, not something punisable by Jews, such as Bais Din!
That case was exactly a case where they could have machnisim oso l’kippah.