A forerunner of the corrido was bandit music, and in El Zarco, this music is described as chaotic. And Altamirano was very worried about bandits, who competed with the liberal state for authority (qué amargura, look at the situation with the narcos now). His real issue is the fuerzas rurales, associated with Porfirio but formed under Benito; they repress opponents of capitalist expansion and they do so independently of the state, like the avenging angel; they have been suppressed in the period Altamirano is criticizing.
The issue is not, however, that one needs paramilitaries. Paramilitary and bandit groups bleed into one another and are recruited from one another, and ultimately the state is at the root of the bandit problem since it had organized questionable characters into improvised, plunderous militias to rout conservative strongmen during the era of the Reforma. (All of this reminds me of Los de Abajo, it does.) So the issue is political and the crux of the matter is sovereignty.
The themes that define the novel are race, nation, law, and republic; Indian (Juárez) and mestizo (Sánchez) join the law of public health and the ray of death (exterminating angel). So (and I must re-study this) the contradictions of liberalism are authority are resolved with this; the “ray of death” is needed because the state is unable to define and enforce a national sense of right and wrong. Law is protected by being suspended, and salud pública takes over when necessary, i.e. law and salud pública are separated.
Sánchez, the mestizo, is the one who does the violence of state formation, and who aids the articulation of nation and state. So the mestizo is not a figure of peaceful reconciliation, but the opposite kind of agent. And yes, contemporary paramilitarism is his legacy. And the novel is interesting because its narrator, and author are so clearly ambivalent about this.