The problem isn't just that kids are getting raped by people in their congregation. The problem's also that anytime someone has "serrious charges" brought against them the elders add notes to that JWs publisher file. And, if the Elders don't take the matter to the police or, as is often the case, tell the victims families not to take it to the police either, this establishes a level of accountability.
Take Daniel Fitzwater for example. He had complaints from 20 seperate witnesses reporting abuse on file at the Watchtower branch. But since none of the complaints met the "two person rule" nothing was done to him.
https://www.youtube.com/watch?v=ywY4mKoubws
(9minutes 40 seconds in)
Who knows how many other repeat offenders the WTBTS has on file. I'm not sure making all official directions come from the CO instead of the branch is going to make the Society any less accountable.