I don't believe that the religion is worth saving--it is too rotten to even try. However, if I had to pick up the pieces, I would first do away with the ban on fornication totally. Only in cases where the act is a result of initiatory force, coercion, or fraud would there be any problem, and then it would be for the initiation of the above. That would stamp out at least 99.99% of the pedophile problem, since most pedophiles within the flock depend on coercion and/or force to complete their dirty work.
Also, that would solve so many other problems. How much of the ban on worldly music and other activities centers on paranoia on fornication? With that rule outdated, all those other rules would no longer have a purpose and could be thrown out. "Modest" dress would also go out the window--if it is very hot, the collar buttons could come undone or even have people wearing comfortable attire. Sisters would be allowed to wear anything (legal, of course) that they see fit, in terms of comfortable mini skirts and pants (according to the weather and other comfort factors). Sloppy attire (and by sloppy, I mean blatant sloppy or filthy and not a scuff mark or wrinkle) would still be frowned on (at least during meetings and service), but people would be allowed to dress comfortably without having to worry about it drawing undue attention to their sexual appeal.
That would also solve a lot of the judicial hearings. No more long, drawn-out hearings where they need to hear every last detail about how far they went. No more hearing about a brother and sister (fleshly) visiting one another without chaperones. In fact, chaperones would be unnecessary for adults, except where such are volitionally desired by all parties. Rape cases would not involve trauma for the victim, since it wouldn't matter if they enjoyed it or screamed and struggled or not. (The perpetrator, on the other hand, since they initiated the use of force and/or coercion, would be subject to legal prosecution and likely a nice long jail term).
I feel that half the problems that the Tower has created stem from this stupid rule against fornication. Do away with that, and half the problems dissolve. Allow and encourage independent research and thinking, and you eliminate pretty much the other half. Eventually, the only rules that are needed are against initiating the use of force, threat of force (coercion), or fraud against others or their property. Do that, and I think the new organization would ultimately succeed.
Fail to reduce the rules to that, and the Tower is doomed and cannot be saved.