Pope Francis appeared on Saturday night to have lost out to powerful conservatives in the Roman Catholic church after bishops scrapped language that had been hailed as a historic warming of attitudes towards gay people.

In the final report of an extraordinary synod on the family which has exposed deep divides in the church hierarchy, there is no mention – as there had been in a draft version – of the “gifts and qualities” gay people can offer. Nor is there any recognition of the “precious support” same-sex partners can give each other.

A paragraph entitled “pastoral attention to people of homosexual orientation” – itself a distinctly cooler tone than “welcoming homosexual persons” – refers to church teaching, saying there can be “not even a remote” comparison between gay unions and heterosexual marriage.

“Nevertheless,” it adds, “men and women of homosexual tendencies must be welcomed with respect and sensitivity.” They should not suffer from discrimination, it adds. But the shift in tone is clear. And, in a potentially stark sign of the discomfort provoked among many bishop, even this watered-down passage failed to pass the two-thirds majority needed for it to be approved.

One hundred and eighteen bishops voted for the text and 62 against. A Vatican spokesman, Federico Lombardi, said the voting numbers had been released at the behest of Francis, who wanted the process to be transparent.

Because the names of the bishops were not released, however, it was unclear whether the paragraph’s failure to pass was due to a protest vote by progressive bishops who had wanted to keep more of the original wording.

At any rate, in a speech to the bishops which received a four-minute standing ovation, Francis showed no sign of disappointment, insisting that disagreement and debate was an intrinsic part of the synod process. “Personally I would have been very worried and saddened if there hadn’t been these … animated discussions … if everyone had agreed with one another or had kept silent in a false and acquiescent peace,” he said.

It was the synod’s other highly controversial subject – considering whether Catholics who have divorced and remarried should be allowed to take holy communion – that included the only other sections to fail to muster the necessary two-thirds majority. Walter Kasper, a German cardinal known in media circles as “the pope’s theologian” because of his closeness to Francis, has been the key backer of a move to allow more people access to the sacraments. But, in an indication of how far his proposal was from gaining a consensus among his global peers, the sections dealing with the thorny issue were guarded and merely noted that there was a clear clash of views. “The question will be further explored,” said the report.

Thomas Rosica, Lombardi’s English language assistant, said the sections without two-thirds majorities had not been “completely rejected”. He stressed that it was “not a magisterial document” but “a work in progress” that provided the basis for another synod next autumn.

The final report will come as a blow to those in and outside the church who had hoped a corner might have been turned in the way Catholic leaders discussed and dealt with homosexuality – even if not even the most optimistic of followers had been expecting a change in doctrine, according to which “homosexual acts” are “intrinsically disordered”.

Francis DeBernardo, executive director of New Ways Ministry, a Catholic gay rights group in the United States, said it was “very disappointing that the synod’s final report did not retain the gracious welcome to lesbian and gay people that the draft of the report included”.

“Instead, the bishops have taken a narrow view of pastoral care by defining it simply as opposition to marriage for same-gender couples,” he told Reuters.

The draft released last Monday had been hailed by some church observers and gay rights groups as “a stunning change” in how the Catholic hierarchy talked about gay people. It had been written with a voice that seemed to echo closely Francis’s own, pragmatically pastoral phrase: “If someone is gay and he searches for the Lord and has goodwill, who am I to judge?”

Exploring the idea of extending mercy to people considered to be in “irregular” situations, it asked whether the church was capable of offering gay Catholics “a welcoming home” and “fraternal space”, admitting that despite “moral problems” associated with them, “homosexual unions” provided “precious support” to each other.

No sooner had it been released, however, than leading conservatives began to speak out against the text. One, American cardinal Raymond Burke, criticised a lack of transparency, saying the mid-point report had not reflected the diverse views of the whole synod.

“A great number of the Synod Fathers found it objectionable,” he said in an interview.

Burke, a leading doctrinal rigorist in the church who had vocally opposed any move to ease the ban on remarried divorcees taking communion, is currently prefect of the supreme tribunal of the apostolic signatura, the Vatican’s supreme court. But he said on Friday he was to be demoted to a lesser post. Asked by the National Catholic Reporter who had made that decision, he reportedly responded: “Who do you think?”

Vatican observers say that, by calling the first extraordinary synod in nearly three decades and encouraging the nearly 200 bishops taking part to speak their minds during the fortnight-long gathering, Francis, 77, has embraced a radically more collegiate style of church governance than has been seen for decades. But although the Argentinian wanted to listen to what the bishops had to say, he may not always have liked what he heard.

Ever since his election last March, he has made clear his belief that the church needs to become more inclusive and understanding of real people’s lives if it is to survive, let alone grow.