"How do JWs reconcile the fact that so many of their GB members are either pedophiles or other morally challenged individuals?"
Well, three GB members out of about 30 have been accused of pedophilia AFAIK, and considering that nothing was ever proven in a court of law, any JW who hears that accusation can easily dismiss it, for better or worse.
When it comes to being morally-challenged, I'm not sure what you mean. It's easy for us to say from the outside that running a deceptive high-control group is morally-challenged, but why would a believing JW think that way? If you mean various other stories about the GB members being rude to people, only a handful of Bethelites would know about any given experience.
Most Witnesses have not been to one of the U.S. Bethel facilities on even a tour, let alone do they actually know any higher-ups who work there. For most JWs, the whole "JW Experience" consists of what they see in their local congregation. Thus, it's easy for them to live in a bubble.