Here the 1840 edition changed the subjunctive were to the indicative was. The was continued in the RLDS textual tradition until the 1908 RLDS edition. As discussed under 1 Nephi 17:31, this 1840 change was probably a typo. In the earliest text, there are 77 instances of “save it were” and only 3 of “save it was”. In each case the critical text will let the earliest textual sources determine whether the verb form should be the subjunctive were or the indicative was.
Summary: Maintain the subjunctive were in Alma 17:38 (“save it were their leader”) since this is the reading of the earliest textual sources for this passage.