The 1906 LDS edition added the perfective had to this verse. That edition was never used as a copytext, so the intrusive had was never added to any subsequent LDS edition. Either reading is theoretically possible, although the reading without the had works better in the larger context since the following text provides the actual words of the covenant (immediately after “we covenant with our God that …” ). The 1906 error seems to have come from the preceding sentence (at the end of verse 21): “even as they had rent their garments”. The critical text will follow the earliest textual sources, which lack the had in “now this was the covenant which they made”.
Summary: Maintain in Alma 46:22 the original reading without the perfective had in the relative clause: “now this was the covenant which they made” (instead of “now this was the covenant which they had made”).