I think the main issue is not the two-witness rule but, rather, Watchtower's failure to encourage that allegations of child molestation be reported to secular authorities by either the victim themselves or the victim's parent or guardian. It's one thing to tell victims/parents/guardians they have an absolute right to report allegations to secular authorities, and it's something else entirely to encourage that this be done.
Otherwise the two-witness rule is essentially the same concept secular law uses for prosecution, only secular law does not ply the term "two witnesses" like Watchtower does. The two-witness rule is something used internally by Watchtower demanding that allegations must have corroboration over and beyond an allegation. Secular law requires corroboration too. Corroboration does not require two human beings be present for and observe an act of molestation, with the victim being one of the "witnesses". In Watchtower's case, the two-witness policy is one requiring corroboration, and corroboration should be required in order to convict a person (in JW speak: disfellowship) of such a crime. Potentially even circumstantial evidence could establish corroboration, but it would have to be precise so that no alternative was left other than guilt of the alleged molestation.
That said, to me the primary issue at stake is Watchtower's failure to actually encourage that allegation of child molestation should be reported to secular law enforcement by anyone with reason to believe the report could be true. If Watchtower is concerned about breaching ecclesiastical privilege it could at least take the step of encouraging that victims/parents/guardians should report the matter to secular authorities. There is no excuse for failing to do the latter. None at all. This failure is, to me, at the very least immoral.