It's not just about good vs evil. It's about love and forgiveness. That's not to say pedophiles should get off scot free, because it's also wisdom - it's very unwise to keep a pedophile in a position where they have access to kids like that.
But I digress. If the org is imploded, all the churchgoers will have to find a new church, and many won't bother. Unless the church has serious theological issues (which just about no church would think they do,) that wouldn't be good. Instead, it's possible to remove the bad apple and replace them with someone else. The way my church's denomination does it, whenever a pastor steps down, the new pastor comes from another church, which helps to make sure there isn't lasting corruption. From what I read about this one, the new pastor is the old pastor's son, so...