Here in the printer’s manuscript, Oliver Cowdery initially wrote “that ye are despised”, but the ink flow for his quill was very broad and rather messy. He either cleaned his quill or sharpened it; then he crossed out the defectively written that and rewrote it supralinearly. In other words, one should not interpret this correction as an attempt to reverse an initial decision to remove the that. The original manuscript is not extant for this part of the sentence, but there is space between extant fragments for the that. The critical text will maintain this instance of the subordinate conjunction that.
This passage also has an unusual typo in the 1953 RLDS edition, namely, the replacement of the preposition of with for in the clause “ye are despised of your brethren”. Clearly, “ye are despised for your brethren” makes no sense here. The text otherwise uses the preposition of or by for this expression:
(The first example is a quotation from Isaiah 53:3 and follows the language of the King James Bible.) The critical text will maintain the use of of here in Alma 32:12.
Summary: Retain in Alma 32:12 the conjunction that and the preposition of in the clause “that ye are despised of your brethren”.