How were the king-men who refused to fight for the cause of freedom punished by Maroni and Pahoran?

They were executed.

Those king-men who had been taken and cast into prison; and they were executed according to the law; yea, those men of Pachus and those king-men, whosoever would not take up arms in the defence of their country, but would fight against it, were put to death. ... Yea, and whosoever was found denying their freedom was speedily executed according to the law. ... Moroni and Pahoran ... inflicted death upon all those who were not true to the cause of freedom. Alma 62:9-11