Mother Teresa is to be made a saint on Sunday, formalising a status that was as good as hers already during her lifetime. The tiny Albanian nun inspired devotion wherever she went because of her transparent holiness and dedication to the poorest of the poor. Her Missionaries of Charity order continues the work she began in Calcutta around the world.

That  Prominent among them was the atheist campaigner Christopher Hitchens, who wrote an extended essay entitled The Missionary Position: Mother Teresa in Theory and Practice, designed to demolish what he regarded as the myths surrounding her. He returned to the charge in a Slate article in 2003, written when Pope John Paul II approved her beatification. In it he described her as a "fanatic, a fundamentalist and a fraud". Hitchens said her work with the sick was tainted by her view that suffering was a gift from God, that she had "spent her life opposing the only known cure for poverty, which is the empowerment of women and the emancipation of them from a livestock version of compulsory reproduction" and was a friend to "the worst of the rich", including Haiti's Duvalier family.

Mother Teresa's interventions in politics have been criticised more widely. She endorsed the appalling rule of Enver Hoxha in her native Albania and even backed Indira Gandhi's suspension of civil liberties in India in 1975, saying: "People are happier. There are more jobs. There are no strikes." She also took money from highly questionable sources, including the publisher Robert Maxwell, who stole hundreds of millions from his companies' pension funds.

Among the most damaging criticisms, however, are those around the quality of care in her hospitals and the alleged ulterior motives of her Missionaries of Charity.

The editor of the British medical journal The Lancet, Robin Fox, visited the Home for Dying Destitutes in Calcutta in 1991 and produced a disturbing report. He said that care was haphazard and that nursing sisters were required to take decisions for which they were not qualified. He said the sisters did not distinguish between curable and incurable patients, and that there was a lack of strong painkillers which he related to Mother Teresa's view that pain was a blessing.

Fox's criticisms were backed up by a 2013 study by a Serge Larivee and Genevieve Chenard of the University of Montreal, who surveyed 96 per cent of the literature on Mother Teresa. They came to the conclusion she was was "anything but a saint", with "her rather dubious way of caring for the sick, her questionable political contacts, her suspicious management of the enormous sums of money she received, and her overly dogmatic views regarding, in particular, abortion, contraception, and divorce".

Another critic is Dr Aroup Chatterjee, a London-based doctor who grew up in Kolkata (as Calcutta is now known) and has also written attempting to debunk her.

Chatterjee collaborated with Hitchens in a sceptical Channel 4 documentary, Hell's Angel, in 1994, and wrote Mother Teresa: The Final Verdict in 2003. An atheist, he objected not only to what he said was bad medical practice, but also to what he saw as the Catholic Church's hidden agenda. He told the New York Times: "I think it's an imperialist venture of the Catholic Church against an Eastern population, an Eastern city, which has really driven horses and carriages through our prestige and our honour.

"I just thought that this myth had to be challenged," he added.

This unease with the missionary agenda of the Mother Teresa sisters, and resentment at how Kolkata has become known for its poverty, is widespread. Sanal Edamaruku, president of the India-based Rationalist International, wrote: "Mother Teresa has given a bad name to Calcutta, painting the beautiful, interesting, lively and culturally rich Indian metropolis in the colours of dirt, misery, hopelessness and death."

Did the Missionaries of Charity have a conversion agenda? According to Hitchens, they were encouraged to baptise people on their deathbeds surreptiously. Susan Shields, a former member of the order, told him: "Sisters were to ask each person in danger of death if he wanted a 'ticket to heaven'. An affirmative reply was to mean consent to baptism. The sister was then to pretend that she was just cooling the patient's head with a wet cloth, while in fact she was baptising him, saying quietly the necessary words. Secrecy was important so that it would not come to be known that Mother Teresa's sisters were baptising Hindus and Muslims."

This is certainly a view held by many Hindu nationalists today. According to the international joint general secretary of one such organisation, the Vishwa Hindu Parishad (VHP), India's Prime Minister Narendra Modi should not be sending a delegation to the Vatican for Sunday's ceremony.

Reported by The Indian Express, Surendra Jain said: "The canonisation of Mother Teresa is an alarm bell that now there would be more conversions in India and more funds [for conversions] would be routed to India."

Mother Teresa first came to the attention of the wider world with the publication in 1971 of Something Beautiful for God, an account of her life and work by the journalist Malcolm Muggeridge. Since then the image of the diminutive figure sustained purely by spiritual power and enabled by God to do mighty works has been irresistible – and the attacks on her have not really succeeded in denting it. She has many defenders who offer robust rebuttals of the criticisms levelled at her and her Missionaries of Charity.

And perhaps just as significant, in terms of her public perception, is the sense among Christians that her critics don't really understand what she was doing. So to criticise her for opposing abortion and contraception, for instance, is to criticise her for not running a secular charity, which she never pretended to do. There's a similar suspicion about those who said her views about pain as a gift from God were reflected in the treatment meted out to her patients and clients: they simply didn't understand what is actually a common trope in Catholic ascetic discipline.

The failings of her hospitals and shortcomings of her nursing staff are harder to excuse. But these, too can be seen as reflecting the overwhelming needs they were faced with, perhaps alongside a large dollop of naivety; a charge of which she was clearly guilty in her relationships with dictators and financial predators.

However, it's hard to avoid concluding that Mother Teresa's greatest crime, in the eyes of her critics, was being a Christian. Certainly her fiercest critics are campaigning atheists. And she is suspect in the world of Narendra Modi's right-wing, aggressively Hindu India, and suspect in the world of international healthcare NGOs. She and her order have a different agenda, and it's troubling for them.

Should she be made a saint? Infallibility is not one of the qualifications the Church looks for, and it's just as well. On the evidence, she made many mistakes. But no one has queried her devotion to her cause, or to her Lord, and she has inspired millions through her words and her example. There might be many worse candidates.

Follow Mark Woods on Twitter: @RevMarkWoods