Claims from the head of the Union Theological College that the purpose of marriage is about procreation were "insulting and hurtful", Naomi Long has said.
The Alliance Party leader said the comments by Reverend Dr Stafford Carson were "wounding".
Mrs Long, a Presbyterian who has been married for 23 years, does not have children.
Dr Carson said marriage has to do with family and procreation as well as love.
His comments came after the Presbyterian Church ruled last week that those in same sex relationships could not be full members of the church.
Now same-sex couples cannot take communion and their children cannot be baptised.
"Increasingly, I feel that there is an unwelcome coolness in the [Presbyterian] church hierarchy that makes me feel uncomfortable," Mrs Long told BBC's Talkback programme.
"When I was wrestling with the issue of equal marriage and how the state should approach this, one of the things that influenced my decision was precisely this argument, that marriage was only about pro-creation."
"Increasingly, I feel that there is an unwelcome coolness in the church hierarchy that makes me feel uncomfortable, and I would want that to change." - Alliance Party leader @naomi_long on the Presbyterian Church's recent decisions. pic.twitter.com/d94VL9hzhQ— BBC News NI (@BBCNewsNI) June 15, 2018
"For the first time in my life, I realised what it was like to be a gay person, where the main personal relationship in your life is judged by those outside it and treated as less worthy and valuable."
Mrs Long wanted to know if her marriage was "less valid " than Dr Carson's.
Asked if she was thinking of leaving the Presbyterian church, she said she "didn't know".
The MLA said what has been happening in the church causes her "great concern " and she often comes away from church services "feeling angry".
She also said that she had personal friends "who felt that coming out [as gay] also entailed having to leave the church".
Speaking on 'The View' programme, Dr Carson, who convenes the Presbyterian Church's doctrine committee, said: "What we are saying is that to live in a same sex relationship does not cohere with the teaching of Christ with regard to marriage and sexuality.
"We believe marriage is much more than just about love. There is a whole structure.
"There is a whole purpose to marriage that has to do with family. That has to do with procreation. That has to do with God's will for us."
The former Alliance Leader David Ford told Talkback that he believed the church was moving "to the right " and that Dr Carson's comments about marriage were "deeply hurtful."
Mrs Long's and Mr Ford's comments came after Lord Alderdice resigned from the Presbyterian Church.