Here both manuscripts have the singular commandment. Theoretically, the plural could be correct (since we know Oliver Cowdery sometimes dropped off the plural s). But in this case, the singular is appropriate: the king has given a single command—namely, that the Lamanites attack the Nephites once more:
This command, of course, is contrary to the covenant of peace that Zerahemnah and his army had made earlier with Moroni (see the account in Alma 44).
In Alma 47:3, we do have the use of the plural commands in reference to obedience to the king: “therefore he gave Amalickiah the command of that part of his army which was obedient unto his commands”. Of course, the reference here is not to the single commandment to attack the Nephites since even this loyal part of the army had not yet obeyed that specific command. So the example of commands in verse 3 does not contradict the use of the singular commandment in the previous verse.
There are other examples in the history of the text where a singular commandment has been changed to the plural commandments in the early transmission of the text. For cases where Oliver Cowdery mistakenly made this change, momentarily in one case, see the discussion under 1 Nephi 3:16, 1 Nephi 4:34, and Jacob 3:5. For each case of variation in number for commandment(s), we follow the earliest text. Here in Alma 47:2, the manuscripts read in the singular, as will the critical text.
Summary: In accord with the reading of both manuscripts, restore the singular commandment in Alma 47:2: “they would not ... obey the commandment of the king”.