Communion of Saints, Communion of Sinners
Sometime back a troubled Catholic asked me why the Church engaged in official persecution of the Jews. He noted there were official decrees of persecution from Church Councils (for instance, Lateran IV) and asked why, when Pope St. John Paul II apologized for such actions, he only referred to "Christians" who mistreated the Jews, when it was, he said, "the Church which officially engaged in a program of hate and persecution of the Jews." Naturally, this left him in considerable anguish of mind concerning the Church's claim to infallibility.
Perhaps the first thing to realize is that my correspondent misunderstood the Pope's distinction between the Church and her members. By "the Church" my friend meant "the hierarchy" and not "the body of Christ in union with the bishops and Pope in succession from the apostles". Given this false conception of the Church, he naturally began with a mistaken notion that the Pope was somehow exempting the hierarchy from the sin of Jewish persecution when he distinguished between the Church and "members of the Church".
In reality, however, when the Pope spoke of "members of the Church" committing sin, he is not exempting the hierarchy from responsibility for sin, for they are members (that is, body parts) of the Church too. The reason for the Pope's distinction between members of the Church and the Church is not that lay people are sinners and clergy aren't (a fact abundantly attested by the sexual abuse crisis) but that the Church--that is the Mystical Bride of Christ--is in some mysterious sense a full participant in the holiness of Christ and is truly without sin, yet the members of the Church--from Pope to dogcatcher--are still on pilgrimage to full participation in that mystical reality.
This is exactly the paradoxical picture presented by Scripture, where Paul castigates the squabbling and sinful Corinthians in 1 Corinthians 6:1-11, yet concludes "But you were washed, you were sanctified, you were justified in the name of the Lord Jesus Christ and in the Spirit of our God." Clearly, it is the New Testament, not John Paul II, that is the source of this curious distinction between the spotless Mystical Bride and the quite spotty members who belong to Her. That is why so much Catholic moral exhortation is, curiously, "Become what you are!" What makes the Church holy is not its highly spotty members, but the Holy Spirit, who is the soul of the Church.
That is why Pope declared that persecution (by, for instance, the fathers of Lateran IV) is a sin against the dignity of the human person and called the Church to penance. For the actions taken against Jews and heretics by Lateran IV were (like the actions taken by Trent to touch up Michaelangelo's "Last Judgment") prudential judgements not protected by infallibility. They are simply actions which, given the state of things at the time, seemed like the best course of action (and which are shown by subsequent reflection to be out of accord with the dignity of the human person). But admitting you are wrong when you were not ever claiming to be infallibly right is hardly a contradiction of infallibility. It is, rather, a confession of sin and an act of repentance, which the whole Church is called to practice in every mass.
What good then is infallibility if an ecumenical council can still err in such prudential judgments? The answer is that the Spirit's infallible guidance presumes that the Church is full of screwups and sinners, just as the presence of a babysitter implies that baby is incapable of navigating through life without constant protection and guidance. All infallibility means is that God won't let the Church define error as doctrine, not that the bishops and Pope are magically given an anti-stupid vaccine, nor that, in matters not having to do with doctrine (such as how to legislate civil arrangements in medieval communities) they will always do the right thing. That's good news, since the mercy of God to this communion of sinners is all that will make us into his communion of saints, the Mystical Bride.