According to prescriptive grammar, the word who(m)soever should take the appropriate case (subject or object form) according to its role within the who(m)soever-clause, not according to its role within the larger sentence. Here the who(m)soever-clause acts as the direct object for the main clause, but since the direct object is fronted (“whomsoever … he caused to be put to death”), its role within the sentence is not easily determinable. Except for the 1953 RLDS edition, the textual sources have consistently maintained the object form whomsoever, the reading of the two manuscripts. The 1953 edition replaced whomsoever with the subject form whosoever, perhaps because readers expect whosoever over whomsoever at the beginning of the sentence. Another possibility is that the editors for that edition decided here that the who(m)soever-word was acting as a subject within the who(m)soever-clause because “who(m)soever of the Amalickiahites” is the antecedent for the relative pronoun that, which acts as the subject in the relative clause “that would not enter into a covenant to support the cause of freedom”.
For each case of who(m)soever, the critical text will follow the earliest reading and ignore the role of this word within the clause or the sentence. Thus here in Alma 46:35, the form is whomsoever (the reading of 𝓞 and 𝓟). For another complicated case like this one, see the discussion under Alma 3:17. Also see the more general discussion under pronouns and under which in volume 3.
Summary: Maintain in Alma 46:35 the object form whomsoever since this is the reading of the manuscripts (as well as all the editions except for the 1953 RLDS edition, which replaced whomsoever with whosoever); the critical text will ignore prescriptive emendations based on the role of who(m)soever within either the clause or the sentence.