Pope John Paul II's conservative views on women's ordination and birth control have led to criticism amid the tributes following his death.
Sister Lavinia Byrne said the next pope would need to handle dissent
Catholic writer Dr Lavinia Byrne said: "We have lost somebody great."
But she said the next Pope must look at the problems of dissent, the position of women and the spread of Aids.
Gay activist Peter Tatchell said the Pope's opposition to condoms to fight Aids "condemned millions to die an agonising, needless death".
Dr Byrne, a former nun, said all the accolades given to the Pope were richly deserved.
But she told BBC Radio the Church had "got very heavy-handed" in condemning her book on the ordination of women..
She called the Vatican a "great structure" which "speaks about human rights and preaches the gospel of freedom but doesn't have a very satisfactory mechanism for dealing with dissent".
"Millions of children in developing countries are orphans; having lost their parents to Aids because of the Pope's anti-condom dogma," Peter Tatchell of OutRage said.
"Pope John Paul II waged a ceaseless war against the human rights of women and gay people - opposing the right of women to control their own fertility, blocking women's equality in the church and endorsing state-sponsored discrimination against lesbians and gay men."
Mark Leech, The Prisons Handbook editor, said he hoped the death of Pope John Paul II would heal conflicting views in the Catholic Church.
"As a human being and, may I say it as a Catholic, I mourn the passing of John Paul II... but thank God he's gone," he said.
"He represented so much of what is an anathema to those of us who have lived in the modern world that he has left behind.
"As a gay man, and as a Catholic, looking forward to marrying my partner under the new Civil Partnership Act that comes into force in December 2005, I hope that his passing will see a new dawn in the Church," Mr Leech said.
He criticised the Pope's belief that wearing a condom was a sin and that homosexuals were immoral.
"I am sad that he has died, but I cannot hide the fact that with his passing I hope we will see a new era in the Church," Mr Leech said.
Anne Quesney, director of London-based campaign group Abortion Rights, said she believed the Catholic Church would not change its conservative view on abortion.
Gay activist Peter Tatchell criticised the Pope's anti-condom stance
"Under John Paul II the Vatican's views on reproductive health and reproductive rights have been consistently extremely conservative," she said.
"He was opposed to any form of contraception including condoms and this, especially at a time when Aids is destroying hundreds of thousands of lives."
She said the Pope's views showed he had "little regard" for women's lives.