Taking Heaven by Storm and the chapter I particularly focused on is his chapter on the conflict about slavery within early American Methodism.
I came across these examples of regional ecclesiastical flexibility:
1. At the 1804 General Conference, the conference approved a proposal to print two versions of the Discipline -- one with the rules on slavery for distribution north of the Carolinas, and one without for the southernmost states. (p. 149)
2. The Christmas Conference of 1784 developed a plan to rid Methodism of slavery. Within six months after the Christmas Conference, the outcry and resistance from southerners led to the indefinite suspension of the 1784 rules. Where and how this happened, I am not sure, perhaps at annual conferences. Maybe the distinction between annual and general conference had not yet become clear. But the action of the general conference was suspended by the outcry of a particular region of the church seemingly between general conferences. (p. 140)
3. The general conference of 1796 passed a motion to allow the bishops to ordain African Americans but it caused such an uproar among southern preachers that it was not printed in the conference minutes or in the Discipline. (p. 140)
3. Just disturbing: The Madison, Kentucky, Methodist Circuit passed a rule that no member of their society should purchase a slave except in cases of mercy or humanity to the slave. If a slave was purchased, the owner should report to the Quarterly Meeting when the slave would be freed. John Bennett was removed from the society for purchasing a slave without the Quarterly Meeting's permission. Next year Bennett reported that he had bought 18-year-old Sarah for $370 and proposed to free her after 20 years. His membership was reinstated. (p. 142)
Maybe the "covenant between the Church and its clergy" was not yet "sacred" at that point of history, but there seems to have been a certain amount of regional flexibility back then.