In the late 1940s Murray began to grapple with the problem of how the beliefs of a pluralistic, democratic society such as that of the United States could be integrated into the teachings of the Roman Catholic church. Murray was an outspoken opponent of censorship on the part of the Vatican, and, indeed, was opposed to any effort by the church to bring about change within states by means other than moral persuasion. Many of his writings on these topics first appeared in Theological Studies, a quarterly journal published by Woodstock College, of which Murray became editor in 1941. By the mid-1950s he was forbidden by the Jesuit order to write on topics pertaining to religious freedom and issues of church and state...
So, it would seem that advocating religious freedom led to John Courtney Murray being censored by the Catholic Church. Rather odd, wouldn't you say, if your characterization is correct?
Thr Fr. Murray story is a fascinating one that the Encyclopedia Brittanica frankly got wrong. The 20th century saw a continuing struggle within the Church between the Modernists and the Traditionalists. Modernism had been declared a heresy bu St. (then Pope) Pius X and all Catholic clergy were required to take an oath against it. Fr. Murray was silenced in 1954 for his public and persistent advocacy of Modernism in direct disobedience to his order, his bishop and the Vatican. He was not excommunicated, just forbidden from publishing and publically speaking on anything not approved in advance.
Fr. Murray was called to Rome to assist in the development of the Dignitas Humanae doctrine in Vatican II. In spite of his contributions Fr. Murray continued his pro-modernist advocacy and, in defiance of the Church took public positions in favor of abortion, birth control, dialog and cooperation with Marxists and a number of hot button issues in the 60's. Had he not died of a heart attack in 1967 he probably would have been excommunicated.
Your Catholic "hero" represented everything you hate about the Church and gave political cover to the likes of Ted Kennedy. The Church is still working to undo the damage he caused.
Peace be with you