In the original manuscript, Oliver Cowdery initially wrote I then, which is an obvious error. Oliver corrected his mistake by crossing out both words and supralinearly inserting by then. The correction seems to be virtually immediate since the level of ink flow is unchanged. The fact that Oliver at first wrote I instead of by was probably due to the preceding occurrences of I in this passage (and facilitated by the phonetic similarity between I and by). Oliver also crossed out the word then, but in his supralinear insertion he simply repeated the then. It is possible that Oliver accidentally crossed out one too many words and thus restored the then.
Another possibility is that Oliver Cowdery misheard some other word as then but that in his correction he accidentally rewrote the incorrect then. By the time Oliver got around to producing the printer’s manuscript, he was unable to recall what by then originally represented. He obviously found by then impossible, so he freely edited the adverbial then to the determiner this. As a result, all editions (including the current text) have by this. I would conjecture that the original text actually read by them. Oliver initially misheard the dictated by them as I then, but this error was caught and partially corrected. Oliver intended, I would propose, to correct I then to by them, but he accidentally wrote then instead of them. There is considerable evidence elsewhere in the manuscripts that Oliver frequently miswrote them as then; in the following listing, I give only the readings in 𝓞 (where extant), 𝓟, and the 1830 edition (represented respectively as 0, 1, and A):
error uncorrected in 𝓞:
error corrected in 𝓞:
error uncorrected in 𝓟:
error corrected in 𝓟:
Clearly, Oliver could have miswritten them as then in his supralinear correction in 𝓞 for Alma 29:11. In the emended reading, by them seems to mean ‘by means of them’. Alma the elder was the one responsible for establishing the church among his own converts as well as later among the Nephites in the land of Zarahemla. For some discussion of the use of by with the meaning ‘by means of ’, see under Alma 27:24.
Summary: Emend Alma 29:11 to read “and by them did establish his church”; neither the initial reading in 𝓞 (I then) nor the corrected reading in 𝓞 (by then) is possible; Oliver Cowdery’s conjectured reading in 𝓟 (by this) was purely speculative on his part and can hardly represent the original text.