Social: The explicit designation of Limhi's people as members of a "church" is not explicitly extended to the rest of the land of Zarahemla. This is a division of naming a belonging. Remember that Benjamin had already convenanted with his people to become "sons and daughters of God" (see Mosiah 5:7). That covenant was to provide the Zarahemlaites with a uniform base of belief, a covenantal means of leveling society (as discussed for Benjamin's discourse). A short generation has passed since that time, and no longer is there a presumption of unity. There is now an explicit structure separate from the rest of society, something that Benjamin's covenant did not do.
The separation of realm of influence now extends to Mosiah himself. Mosiah grants to Alma the power to ordain priests and teachers over each "church." Effectively this diminishes the regnal power of Mosiah, as he is now removed from an essential role in the religious institution of his society. While Mosiah would certainly be titularly the head of the "church," he was no longer the effective leader of it. That position passed to Alma.
As noted earlier, the influence of Alma is tremendous. With the implications of Alma's position in Nephite society, and the rapidity with which he acquired that position, we can only wonder at the personal charisma he must have had to so completely imbue Nephite society with his own ideas on religion and government (we will see the ideas on government appear in the future - at this point, it is his religious reforms that are most apparent).