That's because back then Indonesia was barely even a state and TNI was barely even a military. The national military was just a concept, what existed then were groups of loosely related and uncoordinated militias with their own agendas. Many are just simply "Naga Bonar" tier, self-proclaimed army part-time, local bandit full time. The government and the military have no capacity to control Indonesian territory, even more so because of the Dutch invasion. So the existence of ideologically motivated radical rogue revolutionary militias was inevitable back then. That is why we even have problems with DI/TII and Permesta, to begin with, as prior to the 1957 standardization campaign regional commanders were semi-autonomous and therefore have regional and golongan loyalty.
That is why I think Ukraine made a mistake here. You said it yourself that such militias are quick to develop into a subversive ideological element, hence the case with Madiun Affair. If Ukraine even gets out of this war alive, we can still expect that there will be a Right-wing coup waiting to happen as these extremist groups are getting influence and experience from the war.
The difference with Indonesia's past case is that Ukraine is a well-established country with an organized national military, unlike revolutionary era Indonesia. But they still go down this path by accepting extremist elements into their armed forces. So it is more proper to compare their case with Germany and their experience with the paramilitary role of SA and SS.
Heck, we can see how the existence of such elements motivated Putin to invade, hence "denazification". This is the same logic with the US supporting PRRI/ Permesta out of fear of Indonesia getting more left-leaning. At first, they might look too small and insignificant just like Permesta, or the Nazis. But then when they finally grow strong, it will be too late, and something extreme will happen sooner or later.