The 1892 RLDS edition replaced had with have in the first relative clause in this passage, but this was undoubtedly a typo since the had was retained in the following relative clause (which parallels the first): “yea in fine because of those who had rebelled against their country and also their God”. The copytext for the 1908 RLDS edition was the 1892 edition; thus this error was carried over into that edition. But the 1953 RLDS edition restored the correct had.
Summary: Maintain the past perfect auxiliary had in both relative clauses in Alma 62:2 (“who had driven Parhoron from the judgment seat ... who had rebelled against their country and also their God”).