Operacion Independencia can't just consist of a roundup of political prisoners, because the army can't risk the lives of its men and lay its prestige on the line simply to act as a kind of police force that ends up by turning over X-number of political prisoners to some timorous judge... who will apply lenient punishment which in turn will be cancelled out by amnesties granted by ambitious politicians courting popularity. We're at war, and war obeys another law: he who wipes out the other side wins."
Operacion Independencia can't simply be a collection of arrests, as the army would be putting its soldiers' lives at risk and its reputation on the line to act like a police force that ultimately leads to lenient punishments being handed down by judges who are swayed by politicians seeking popularity. In times of war, only those who defeat their opponents emerge victorious.