The 1902 LDS missionary edition accidentally replaced the past-tense had with the present-tense have, an obvious typo since all the preceding language is in the past tense: “there was continual peace … their heed and diligence which they gave unto the word of God which was declared unto them”. The 1902 edition was never used as a copytext, so this error was never copied into any subsequent LDS edition.
Summary: Maintain throughout Alma 49:30 the past-tense verb forms, including the had in “those which had been ordained by the holy order of God”.