I don't really get the Cheney comparison. Cheney essentially commanded the safest superpower on Earth at a time when there was no real threat. Cain is in command of a Battlestar that could be annihilated at any moment by a horde of killer robots that outnumber them severely.
She has much more right to make the tough choices. Choices that are generally rational because unlike Galactica, Cain doesn't have Gods and angels saving her ass or leading her to safety all the time.