The 1874 RLDS edition added the subordinate conjunction that in this passage, perhaps in an attempt to help the reader interpret the nonparallel conjoining of a gerundive clause (“Alma and Amulek coming forth out of the prison”) with a finite clause (“the walls thereof had fallen to the earth”). The addition of the that makes it clear that the finite clause “the walls thereof had fallen to the earth” should be interpreted as a subordinate clause. Nonetheless, the 1908 RLDS edition, following the reading in 𝓟, restored the original text without the intrusive that. In addition, David Calabro points out (personal communication) that the conjoined finite clause could be treated parenthetically:
The printed editions have always had commas surrounding this finite clause, but not dashes or parentheses. In any event, the critical text will maintain the original reading here in Alma 14:29, no matter whether the finite clause is treated parenthetically or as part of the direct object for the verb saw.
Summary: Maintain in Alma 14:29 the finite clause “the walls thereof had fallen to the earth” without any overt that conjunction that would force the reader to interpret this clause as a subordinate clause rather than as a parenthetical main clause.