The Rt Rev John Chalmers, Moderator of the General Assembly of the Kirk, delivered a ground-breaking speech apparently partly addressed directly towards traditionalists.
He urged those unhappy with the move towards greater acceptance of ministers in civil partnerships against a knee-jerk reaction.
Mr Chalmers, who holds the role of Moderator for a year, made the strongly worded call to the near-800 invited Kirk members yesterday at the final day of the week-long annual gathering in Edinburgh.
His comments came at the end of an assembly that agreed to further consider allowing gay clergy, sparked by the appointment of the Kirk's first openly gay minister in 2009 to an Aberdeen church. Since then 13 ministers out of 1389 congregations have quit on the issue.
Mr Chalmers asked for unity over the issue that has divided Kirk members and outlined other critical issues.
He urged those considering leaving over the stance on gay ministers to "think again".
He said: "Over the last two years I have patiently absorbed much of the rancour by a very few who have set out their stall for leaving the Church of Scotland, but before anyone thinks any more about leaving the Church of Scotland I ask them to think ecclesiologically. Do not mistake what some call the 'church family' for the comfortable, settled, agreeable fellowship that you belong to.
"The 'church family' is greater than that - it is generations-wide, it is worldwide, it is theologically wide. The Church of Jesus Christ has never been a place of such easy safety and security."
He went on: "Ask those who want to leave, to let you know when they have settled in the perfect church and we will all come round and inspect its credentials.
"I'm not sure, however, how long we can go on without addressing ourselves to a more adequate way of describing our width as measured against what we call our subordinate standards."
He said the need for unity is highlighted by the facts that: "A quarter of our charges do not have an inducted minister; we only have two ministers under the age of 30, when I was inducted there were seven of us in my presbytery; four times the number of ministers will retire in the next six years than we are likely to recruit in the same time-frame".
He said: "A tide has to be turned because a generation of people out there are being invited to live a life of disbelief - if not unbelief. And there is no justification for that.
"This Church of ours has to stop its navel-gazing, get out from under subjects that no one is actually talking about and get out there and capitalise on the fact that people still want purpose and faith in their lives, they just need it to be: accessible, relevant, generous, forgiving."
The assembly agreed during the week to move towards further consideration of the acceptance of gay clergy, and a push against pockets of local sexism in the Kirk to be broached.
The assembly also held a unique debate on independence involving theologian Rev Doug Gay and Labour MP Douglas Alexander.