It seemed like business as usual at the Vatican yesterday as Rome firefighters fitted a chimney on the top of the Sistine Chapel for the puff of white smoke which will herald the election of a new pontiff by the conclave.

However, it will be clerical sexual abuse, financial scandal and homosexuality that top the agenda for the 115 cardinals as they reflect on the role of the Roman Catholic Church in the modern world under Michelangelo's towering depiction of the Last Judgement.

An American activist group has ensured that sexual abuse remains a lead issue by publishing a list of 12 cardinals it says should not be considered for election, claiming they had a poor record in handling cases of priestly paedophilia, or had been negligent in oversight. There is no allegation any of the 12 cardinals were involved in any criminal acts themselves.

The blacklist, published by Survivors Network For Those Abused By Priests, included several candidates thought to have a real chance of lifting the pope's white "zucchetto" hat.

Among them are Italy's Angelo Scola, a reformer believed to be capable of taking on the curia, Canadian Marc Ouellet, head of the Vatican's powerful Congregation for Bishops who had initial responsibility for handling the resignation of Cardinal Keith O'Brien, and the Boston Franciscan, Sean O'Malley.

Cardinal O'Brien's departure as primate of the Catholic Church in Scotland and his admission that he had inappropriate sexual relations with young priests and students under his authority also helped to keep clerical morals centre-stage in the most media-exposed papal succession ever.

"It's the first time a cardinal has declined to participate in a conclave because of accusations that have put him in difficulty in front of public opinion," said Marco Politi, an experienced Vatican-watcher who writes for Il Fatto Quotidiano newspaper. "There may also have been pressure from the Vatican, but it's without precedent.''

The Vatican expert noted that O'Brien had initially resigned as archbishop while contesting the allegations against him, subsequently admitting that his sexual conduct had "fallen below the standards expected of me as a priest, archbishop and cardinal".

Politi wondered whether that meant there were more recent accusations against him than those brought to the attention of the papal nuncio in London by four alleged victims, which relate to events that took place some 30 years ago.

The Vatican's official spokesman has said little about the details and timing of the allegations. "We have already told you all we know. We don't want to spend all week talking about Cardinal O'Brien," Father Federico Lombardi said.

Christine Anderson, a Catholic nun who teaches management skills to senior Vatican officials, has fond memories of working with O'Brien at the Craighead Institute, which she founded in Glasgow in 1987.

''It took courage to admit his failings and say sorry," Anderson said. "Who among us doesn't have a sin?" I wish he would come to Rome to the conclave, to be the conscience of others."

That became formally impossible on Friday, when a general congregation of cardinals accepted his letter of apology, citing "personal reasons", for not attending.

A member of the Faithful Companions of Jesus (FCJ), Anderson said O'Brien's comments, particularly on ending celibacy, had made him many enemies. However, his condemnation of homosexuality has cast him now as a hypocrite, while his willingness to discuss priests' celibacy infuriated conservatives in the Vatican.

As far back as 2002, O'Brien told the Sunday Herald in an interview: "I have no problems with celibacy withering away. There is no theological problem with it ending. The loss of celibacy would give liberty to priests to exercise their God-given gift of love and sex rather than feeling they must be celibate all their lives." He reiterated his comments earlier this year when he said priests struggled with celibacy and should be able to marry.

Anderson said: "In the past, several parish priests would live together in a rectory. Now most of them live on their own. It's a very lonely life. What he said about celibacy: it was a wonderful thing to say at the end of your ministry."

Anderson is not the only observer to suspect there may have been a hidden agenda behind the Vatican's rapid acceptance of O'Brien's departure, and that it could be connected as much to his unorthodox view on the possibility of married priests as to his personal conduct.

A former priest, who studied at the English College in Rome in the 1970s and left to get married, said the Vatican had shown itself to be more exercised by dissent on doctrinal matters than the personal failures of individual priests.

"In the event of priests misbehaving or financial irregularities they try to sweep it under the carpet, to avoid scandal," he said.

"I wouldn't be surprised if O'Brien's comments on celibacy played a role in his removal. A 'loose cannon' talking to another 114 cardinals in the conclave would be alarming to conservatives."

Church conservatives have indeed been outraged by the cardinal's comments on celibacy, seen as violating an oath to uphold traditional teachings that O'Brien pronounced before being made a cardinal, and failing, in their view, to recognise the depth of the church's theology on celibacy – a sacrifice made for the love of the church and of Christ.