The Amalickiahite threat was not one of simple belief, but one of treason against the foundation of the Nephite religion and politics. Moroni determined that having a number of apostate and traitorous Nephites joining with the Lamanites would not be wise. He had recently fought a war that began with the Zoramites in Antionum apostatizing and joining with the Lamanites. Moroni clearly had no desire to repeat the number of deaths that resulted from that battle.
Moroni cuts off the people fleeing with Amalickiah, although Amalickiah himself and a few others escape and will indeed unite with the Lamanites. At this point, however, the majority of the Amalickiahites were captured.