Although the change of then to than in this passage is not a substantive change, it represents editing on the part of Oliver Cowdery. Here he proofed the 1830 signature (number 22) against 𝓞. In this case, he decided to correct 𝓞 itself to agree with what the compositor had set, thus correcting in pencil the spelling of then by overwriting the e with an a. Oliver made a number of changes in pencil in 𝓞 for this part of the text (signature 22 covers Alma 41:8–46:30), although this emendation in 𝓞 is the only nonsubstantive one. For a list of these secondary changes in 𝓞, see under Alma 42:31.
For this particular instance of than, Oliver correctly wrote than in 𝓟. The critical text will follow the standard spelling; for discussion regarding the spelling then in place of the standard than, see under 1 Nephi 4:1 as well as more generally under than in volume 3.
Summary: Follow the standard spelling than even though it was occasionally spelled then in the manuscripts.