There is always a way to clean up the Church: PRAYER!! and Fasting and Sacrifice. Just because no one has devised a program to do it, does not mean that Jesus can’t. We who are faithful are being called to suffer, and it is not for us to ask why, any more than we should ask why Jesus had to suffer for us on the Cross.
Rather than being evil Herself, I believe that the Church, the Bride of Christ, has been raped. It can’t be undone, but it can be healed and Christ can heal the Church, just as He heals us. It will take a lot of time and a lot of prayer and a lot of suffering, but in the end, the Bride of Christ will be glorious and spotless once again.