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In the congregations I have been involved in, each situation ends differently. I had the misfortune of being around during four cases in three congregations.
Cong. #1: In the late 70's a MS molested his eldest granddaughter (he had two under 5, but I don't remember if the youngest was also involved). He was reported to the authorities; served weekend jail time. The congregation publicly reproved him since he was repentant. In the local needs talk, the men were warned to watch their sexual desires. Then the wives were admonished to provide marital due so that their husbands wouldn't be so inflamed that they would commit immorality. You see, this MS had a sick, bedridden wife, and so he turned to his granddaughter to satisfy his sexual appetite. He explained to the elders that it was partly his wife's fault, and he was sorry, so he just got public reproof. We were also counseled that we were supposed to accept this discipline as being from Jehovah and treat this brother as before. To shun him would be wrong (no matter how repulsed we were). Six months later he had full privileges again.
Cong #2: MS was accused by his wife of molesting their oldest daughter (under 5). He went to jail, had to have supervised visits, and the daughter had psychological counseling. In this counseling the therapist was able to discover exactly what had happened through using anatomically correct dolls. The incident almost split the congregation due to the popularity of this couple. Some sided with him, some with her. She took the girls and left him and the "Truth", and eventually got a worldly boyfriend. Of course, then the congregation was back in the man's camp and they all believed that the woman had been having a secret affair with this boyfriend all along, and had coached her daughter in what to say just to keep custody of her girls when she left her husband and the truth for this other man.
Cong. #3: MS went to prison for abusing a young boy. The elders questioned him, and he admitted it. He was disfellowshipped.
In a separate incident, a former elder, known for being a very controlling and strict parent, was accused of raping three of his six daughters when they were very young. These three were now grown and married, but only one could recall the events clearly. She was his accuser. The elders, due to their being only one witness against him, had to let him go. Nothing was done to this man. The daughter who was his accuser, and her two young children, died about a year later in an accidental death where she crossed the center line and collided with a cement truck. The family and cong. insisted that it was due to insulin shock, but the police found no evidence of it. I know even more about this case, but can't reveal it in this forum.
So sometimes the system works, and sometimes it doesn't, to the frustration of many, including sometimes the elders who want to do the right thing, but whose hands are tied by the two witness rule, the Watchtower legal department, and the decisions of other elders in the congregations.