The Lord explicitly accepts Alma's churches. Perhaps the recent events had raised some question in Alma's mind about the wisdom of the churches since they appear to have engendered divisions as a side effect. The Lord may be allaying those fears by telling Alma that his establishment of the church is accepted.
The most significant part of this passage is the final statement concerning the church. God notes that "they shall be my people." This is the covenantal promise. The Lord is reaffirming the covenant, but that covenant has been shifted from the community to the church community. The covenant now does not reside in lineage, but in the authority and ordinances of the church.