He argued a similar clause existed in the recently passed Marriage Amendment Bill, whereby ministers were not obliged to solemnise a marriage if it would contravene the church's religious beliefs.
While Professor Rishworth said the church was not above the law, he argued it should be exempt from state interference when selecting its leaders.
The church's canons were of "divine origin" and the church should be allowed to practice religious autonomy when carrying out the important task of appointing leaders, he said.
Bruce Gray QC, also representing the church, acknowledged there were widespread frustrations with the slow progress the church had taken with issues such as homosexuality.
However, the Anglican flock were a "disparate group" and any appointed leader needed to represent the "pathfinders" at the front of the flock, as well as those at the back, he said.
Tribunal chairman Rodger Haines, QC, reserved the panel's decision, pending further submissions.
Bishop Bay said outside Auckland District Court today that he was very conscious of the human impact of the case.
"We are dealing with sensitive issues and with the human lives that are affected by them."
The Anglican Church had been engaging in progressive discussions as to whether there would be any changes following Mr Sisneros' case, however it was up to the church's governing body.
Mr Sisneros, also speaking outside the hearing, said he appreciated that the tribunal had taken the time to hear his complaint.
"It's a comfort in knowing that we have already made an important concession from the church.
"Not allowing gay and lesbian Anglicans who are living in same-sex relationships to test their calling is discriminatory."
Mr Sisneros, a 38-year-old American who holds New Zealand residency, said he was grateful he lived in a country which provided a forum like the Human Rights Tribunal "where marginalised people can have a voice and be heard".
