Christ entrusted the leadership of His Body, the Church, to humans. With human freedom, a much greater opportunity for glorifying God is possible. The Church, made up of humans, gives great glory to Christ when all Her members are acting in a communion of holiness. Unfortunately, in order for us to freely choose, the obvious consequence is that some members of Christ's body will reject the graces that are lavished upon us. In other words, human failure is an unfortunate reality of human free will.
The most natural reaction to witnessing grave moral failings within the Church is to feel hurt or betrayal, maybe even anger. But we must ask ourselves...to whom is our anger directed? Are we angry at Holy Mother Church whom Christ has given to us as the way of salvation, or are we hurt and saddened by one particular person or group who has become enslaved by the snares of sin? Seeing things as Christ sees them helps us to achieve this clarity.
It is the difference between Martin Luther's revolt out of hatred and suspicion and St. Charles Borromeo's faithful implementation of the great reforms of the Council of Trent. One leaves a bloody mess, while another applies the salve of Christ.