The 1830 typesetter deleted the perfective had, probably by accident. Elsewhere in the text, after “did (do) … as” and before commanded, used in the active, there are six occurrences with had and two without:
(Also see the discussion under Omni 1:13, where the had was momentarily lost when copying from 𝓞 into 𝓟.) Since either reading (with or without the had ) is possible, the critical text will accept in Alma 17:34 the reading with the had (the reading of the earliest extant source, the printer’s manuscript).
Summary: Restore the perfective had in Alma 17:34, the reading in 𝓟: “therefore they did as Ammon had commanded them”.