When Cardinal Keith O'Brien stepped down last week, he might have hoped that the furore over allegations of sexual misconduct would swiftly conclude. After all, he was leaving his position as the head of the Catholic Church in Scotland, forgoing his right to attend the papal conclave, and retiring from public life.

In the circumstances, however, denial and retreat were – quite rightly – insufficient. One week on, Cardinal O'Brien has now conceded that, contrary to his initial claims, his sexual behaviour did, indeed, "fall beneath the standards expected". It is not yet clear whether this admission extends to the specific accusations from one former and three serving priests that precipitated his departure. But he has made a general apology. And the Vatican will now investigate – albeit behind closed doors.

The spectacle of a person forced to confront his demons in the full glare of publicity is a discomfiting one. But even that cannot moderate the charges of hypocrisy the former Cardinal must face. That he appears to have broken both his vow of celibacy and the Church's prohibition on clerical homosexuality is a matter for his own conscience. That he used his pulpit to launch vitriolic attacks on gay rights is another matter altogether. After last weekend's mea culpa, the motivation for such harangues is now clear; but their impact is no less pernicious.

Nor does the fallout begin and end with the former Cardinal. The Catholic Church, too, has questions to answer. There is, of course, a chasm between the charges levelled against Cardinal O'Brien and the accusations of child abuse that have rocked the Church in recent years. But the institutional reaction looks much the same. High-ranking churchmen talk resignedly of individual "sinners", yet no responsibility is ascribed to the organisation that shielded their activities from prying eyes. Cardinal O'Brien's transgressions offered the Church an opportunity to show that self-protection does not override the rights of the innocent. It is not being taken.