If we read verses 4 and 5 in isolation from Moroni’s letter to Pahoran, we might think that when Moroni raised the standard of liberty again that it was a declaration of political preference. It certainly had those overtones, for there was only the slightest separation between religion and politics. However, as has been noted before, Moroni’s prime considerations had to do with the covenant of the land. Preserving liberty was to preserve the Nephtie ability to keep their covenants, and keeping those covenants was essential to their preservation in the land.
Thus, the people really did “take up their swords in defense of their freedom, that they might not come into bondage,” but the nature of their freedom was deeply rooted in their ability to worship God and keep His commandments.