The concept of a church was new, and the way it integrated into the larger society was also both new, and unexamined. When the first issue arises, Alma takes it to King Mosiah, even though Alma has been made the head of the church. Under the previous understanding, it would certainly be an issue for the king. When all religion was determined by the community, the king was the head of the religion regardless of the religious officiators.
The concept of the church created a new way of thinking, and created religious issues as separate from social and non-religious legal issues. Since the law had been given by Moses and codified by kings who acted as the religious leader, it would have been difficult to understand how the law applied to issues of these new church organizations.
King Mosiah defines the new relationship by declaring that church matters are no longer kingly matters. They are part of the church itself, not the overall government. There is, for the first time in the Book of Mormon, a separation of church and state. Alma, as the high priest, is designated as the proper person to deal with church issues.