I believe Elders allow pedophiles to roam free in the congregations for many reasons. The main problem is the strict chain of command in the religion, theocratic order demands that they follow procedures. Since the Watchtower is invested in pretending they do not have pedophiles (or if they do it is a very, very tiny number), they are primarily concerned with not bringing reproach on "Jehovah's organization". Elders who do not follow procedure are removed.
In addition, elders are very poorly trained compared to paid clergy. Most lack a college education, so they have ever little understanding of human psychology or pedophilia. Most pedophiles are adept liars, as they have learned to manipulate others to get access to children and they are good at inventing excuses for their behavior ("she came on to me").
The two witness rule is a gift to pedophiles, as they are not usually caught in the act. Even if a child makes a complaint they are not usually believed because people have a hard time believing that someone they know and like could do something like that.
Even when they have evidence or a confession, they may still see it as a spiritual failing, a mistake. If the person expresses remorse and promises to never do it again, they are many times fooled into thinking the problem has been fixed. They don't understand that an attraction to children is deeply ingrained, no matter how sorry the individual feels, or how hard they try to suppress their urges, they will always be at risk to offend a gain. A person like that should never be allowed access to children.
I had a close friend whose son was molested by a brother. He confessed and was reprimanded. Shortly thereafter he became engaged to a sister with children. My friend got in trouble for warning the woman her children were at risk. As far as the elders were concerned, he had confessed and been forgiven. They probably thought everything would be fine because he had a woman now and wouldn't turn to children for sex.
Pedophilia is an uncomfortable subject to talk about, it is sometimes easier to ignore or play down signs or evidence of abuse. It is a problem not unique to the JWs, you hear of similar cases in the school system and other organizations. Jerry Sandusky molested boys for years despite the fact that he had been caught in the act, and many people had reason to believe there was a problem. It's usually just easier to pretend you didn't see what you saw.
I believe most elders have good intentions, it's just that they don't know what they don't know. The real evil is the Watchtower, as they do know what they are doing and know they are putting children at risk.