In the printer’s manuscript, Oliver Cowdery initially wrote “have had done”, then later crossed out the had with heavier, darker ink flow, probably when he was checking the printer’s manuscript against the original. He made two supralinear insertions later on this page of 𝓟 using the same heavier, darker ink flow. See Omni 1:6 for discussion regarding these corrections.
It is possible that in verse 2 the original manuscript (which is no longer extant here) read “as I had ought to have done”, which would mean that Oliver initially put the had in the wrong place but that in his correction he simply deleted the had rather than placing it before the ought. In the Book of Mormon text, the clear majority of examples of the modal verb ought originally read had ought (30 cases, with variation in word order as well as the possibility of occurring with not). But based on the earliest text, there are six cases of verbal ought for which there is no had:
Only the last example is extant in 𝓞, and there the text reads without any had. This last example also occurs without any not, just like the reading in Omni 1:2. The critical text will maintain the six instances of ought that occur without had in the earliest text, including here in Omni.
Summary: Retain the use of ought rather than had ought in Omni 1:2; although originally the majority of instances of ought in the Book of Mormon text occurred with had, a few did not.