Many Presbyterians jubilantly proclaimed that the Holy Spirit had unquestionably descended upon the Presbyterian Church USA’s 221st General Assembly when commissioners voted to amend the definition of “marriage” in the Book of Order, the PCUSA’s constitution, from a union of “a man and a woman” to a union of “two people,” with an overwhelming 61 percent of commissioners in favor for the amendment and 39 percent in opposition to it (out of 565 commissioners total).

The Holy Spirit took a long time coming (if indeed her absence is to blame for the church’s heretofore recalcitrant attitude toward its lesbian, gay, bisexual, transgender and queer, or LGBTQ, brethren), but it’s the only way that the vote affirming and blessing the loving coupling of same-sex Presbyterians could have happened.

This recent vote is a welcoming change of heart from the church’s 1991 and 2008 rulings prohibiting Presbyterian clergy from performing same-sex marriages. When some clergy performed same-sex marriages anyway, the church’s retribution was both draconian and antithetical to any cleric’s sense of fairness and justice. For their commitment to their values, these brave ministers — straight and gay alike — endured ecclesiastical trials as the church considered four possible censures: rebuke, rebuke with rehabilitation, temporary removal from the church, or permanent removal from church office, meaning defrocking.

While homophobia is nothing new in the hallowed halls of most churches, in many ways the Presbyterian Church USA, born out of a liberal Protestant Christian tradition, descending from the branch of the Protestant Reformation begun by John Calvin, had been an embarrassment to itself.

For more than three decades the PCUSA had been engaging more in holy war than in spiritual discernment over the issue. And after the recent vote to amend the Book of Order to recognize same-sex marriage, some Presbyterians are digging their heels even deeper into either the church’s old ways or their own interpretation of God’s opinion on the matter.

“My heart breaks,” the Rev. Steve Wilkins of the New Harmony Presbytery in South Carolina shared with The New York Times during the debate. “I don’t think it’s up to us to change the definition of marriage; in fact marriage has been defined by us and revealed to us in God’s word.”

Sadly, Wilkins is not the only voice crying out against the church’s recent vote. So are many Christians across denominational lines.

Rev. Jeff S. Nelson, a gay ordained minister in the Unitarian Universalist Church and a former Seventh Day Adventist, had concerns about how to console and counsel his former minister and Pathfinders scoutmaster. (Pathfinders is the scouting program for Seventh Day Adventist boys and girls.) In a text exchange with me, he shared his thoughts:

Rev. Nelson: Morning Irene – So whatcha think of those Presbyterians?! 😀

Me: A long time coming with so many of my colleagues defrocked along the way.

Rev. Nelson: Perhaps some truth and reconciliation can restore Justice… Methodists next?

Me: Let’s pray they follow indeed.

Rev. Nelson: Amen… Right now I’m trying to figure out how to witness to an old Pathfinder counselor who is “saddened” by the news. It is painful to hear loved ones tainted by fear… And I must be careful how I choose my words…

Rev. Nelson: Umph.. Good luck!

In 2011 many Presbyterians were indignant when commissioners at the General Assembly voted in favor of ordaining non-celibate LGBTQ ministers, which resulted in breakaway churches.

It is the church’s governing body that calls the shots. And it’s the governing body that has held both civil-union and marriage-equality states — even queer-friendly Massachusetts — hostage to their Directory for Worship in the Book of Order, impeding 9,777 church officersfrom faithfully serving all God’s children.

The advocacy group More Light Presbyterians gives us hope. It is a coalition of congregations and individuals in the Presbyterian Church USA who are committed to increasing the involvement of all people in the church, regardless of sexuality. Their mission is to achieve the full participation of LGBTQ people of faith in the life, ministry, and witness of the church. They were instrumental in successfully lobbying for the vote to allow same-sex marriage at the latest General Assembly.

But before the Presbyterian Church USA gives itself congratulatory pats on the back, let’s remember that the amendment will only become church law if it’s approved by a majority of the 173 presbyteries. The church may proudly identify as “reformed and always reforming,” but let’s hope that the Holy Spirit shows up again to help it along.