I think Cain was cut off from anything
that usually keeps the military in check. She had no superiors whatsover, let alone civilian ones. And there was no civilian society she and her crew were embedded in or connected to.
So, for all intents and purposes she was the commander-in-chief for a community of people which (as far as she knew) solely consisted of military personnel at this point. Which effectively resulted in Cain assuming a rather totalitarian point of view.
She expected that everybody
followed her orders without question and when anyone disagreed with that he or she got quickly eliminated
from the community she led.
In essence, Cain stopped acting like a military commander from a democratic society (something Bill Adama admittedly struggled himself with at times, just not that radical extent) and started behaving more like a military official from, let's say, North Korea.