Jones, the son of a Sydney convict, donated land and money for Otago's first church, St John's Anglican Church at Waikouaiti, north of Dunedin, and arranged a generous endowment for its support.
A recent judgment of Justice David Baragwanath, after St John's church warden Elizabeth Inglis sued the Dunedin Diocesan Trust Board in the High Court at Dunedin, said the case partly concerned the relationship between the church building and the pastoral activities of the church community envisaged by Jones in his deeds of trust.
Different priests, based in Dunedin, had performed services and pastoral care for the small number of worshippers at Waikouaiti (16 regulars) and Palmerston/Hampton (15).
The Bishop of Dunedin, George Connor, had tried to bring the people together by having one priest living in the community to serve both groups, but there had been problems, Justice Baragwanath said.
Counsel for Ms Inglis argued that income from two Jones trusts could be used for church building repairs and funds from one, known as the Glebe Trust, was to be used for clergy in the Waikouaiti area and not for the benefit of the diocese generally.
But a 2005 letter from the Diocesan Trust Board said the terms of the trusts reflect Jones' vision of ministry, rather than support of "bricks and mortar".
"We note that one of the trusts provides for allocation of money to ministry elsewhere in the diocese, in the event of a surplus once the needs of ministry in the Waikouaiti area are fully funded," it said.
"However, it is not the board's intention to do so." Justice Baragwanath said the Glebe Trust Fund may be used for supporting clergy whose major focus was Waikouaiti. Before making decisions, it would be prudent for the trust board to consult St John's parishioners as well as receiving guidance from the bishop.
While neither fund was meant for church maintenance, without an application under the Anglican Church Trusts Act, "proper maintenance is germane to the spiritual well-being of the parish".
While the funds were intended to support clergy whose major focus was Waikouaiti, that did not "limit their outreach" from there.
Justice Baragwanath noted Jones was "determinedly non-sectarian", also making land grants and donations to the Presbyterian, Catholic and Methodist communities and, giving the Anglicans land in Dunedin on which St Paul's Cathedral was eventually built.
