In the part of the Book of Mormon where we first read that Alma was the "founder of their church," the pronoun their refers only to the people who were with Alma in the wilderness; it does not refer to the entire Nephite nation. Thus when the statement is read in context, the true meaning is clear; this meaning is also clarified later in the record when it states that King Mosiah gave authority to Alma over the churches in Zarahemla. (Mosiah 26:8.) A brief historical setting of this period is provided by Joseph Fielding Smith in his answer to the question "Did the Nephites Have a Church Organization before the Days of Alma?"
It should be remembered that Alma had been one of the priests of King Noah in the land of Lehi-Nephi. It should also be taken into consideration that the colony in that land separated themselves from the main body of the Church in Zarahemla. In the days of Amaleki, who kept the Nephite record, a company of Nephites under Zeniff desired to occupy the land which was first settled by the Nephites, and entered into an agreement with the Lamanites to possess that land. There they established an independent kingdom which they possessed for many years, however in constant war and bondage to the Lamanites. In course of time, under King Noah, they became very wicked. It was at this time that the prophet Abinadi was murdered, and Alma, having accepted the teachings of Abinadi, gathered around him all who were willing to keep the commandments of the Lord, and doing so he brought upon himself and his followers the wrath of the wicked king, and they had to flee from their homes into the wilderness, with the intention of making their way back to the land of Zarahemla. The story of their flight, suffering, and blessings from the hand of the Lord were recorded in the Book of Mosiah. While in the wilderness Alma organized his group of believers into a branch of the Church and is spoken of as their founder.The main body of the Nephites, under the second King Mosiah, was still intact in the land of Zarahemla. The reference stating that Alma was the founder of their church has reference only to the refugees who were fleeing from the land of the Nephites' first inheritance. In course of time they found their way back to the main body of the Church and Alma was consecrated as the high priest over the Church in all of the lands occupied by the Nephites. (Answers to Gospel Questions, 3:39-40.)